Linux version Using ReadLine Using Boost Running 64Bit Version mothur v.1.40.2 Last updated: 4/23/2018 by Patrick D. Schloss Department of Microbiology & Immunology University of Michigan http://www.mothur.org When using, please cite: Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. Distributed under the GNU General Public License Type 'help()' for information on the commands that are available For questions and analysis support, please visit our forum at https://www.mothur.org/forum Type 'quit()' to exit program Interactive Mode mothur > set.current(processors=12, fasta=180802_pratima.files.trim.contigs.pcr.fasta, group=180802_pratima.files.contigs.groups) Using 12 processors. Current files saved by mothur: fasta=180802_pratima.files.trim.contigs.pcr.fasta group=180802_pratima.files.contigs.groups processors=12 Output File Names: current_files.summary mothur > summary.seqs(fasta=current, group=current) Using 180802_pratima.files.trim.contigs.pcr.fasta as input file for the fasta parameter. Using 180802_pratima.files.contigs.groups as input file for the group parameter. group is not a valid parameter. The valid parameters are: fasta, summary, contigsreport, alignreport, name, count, processors, seed, inputdir, and outputdir. Using 12 processors. [ERROR]: did not complete summary.seqs. mothur > summary.seqs(fasta=current) Using 180802_pratima.files.trim.contigs.pcr.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 3 3 0 1 1 2.5%-tile: 1 21 21 0 3 56 25%-tile: 1 98 98 0 3 559 Median: 1 98 98 0 3 1117 75%-tile: 1 98 98 0 3 1675 97.5%-tile: 1 98 98 1 4 2178 Maximum: 1 250 250 6 63 2233 Mean: 1 95 95 0 3 # of Seqs: 2233 It took 0 secs to summarize 2233 sequences. Output File Names: 180802_pratima.files.trim.contigs.pcr.summary mothur > get.current() Current RAM usage: 0.00692368 Gigabytes. Total Ram: 125.888 Gigabytes. Current files saved by mothur: fasta=180802_pratima.files.trim.contigs.pcr.fasta group=180802_pratima.files.contigs.groups processors=12 summary=180802_pratima.files.trim.contigs.pcr.summary Current default directory saved by mothur: /home/diddyserver/Desktop/pratima/ Current working directory: /home/diddyserver/Desktop/pratima/ Output File Names: current_files.summary mothur > set.current(fasta=180802_pratima.files.trim.contigs.fasta, 180802_pratima.files.contigs.groups) 180802_pratima.files.contigs.groups is not a valid parameter. The valid parameters are: processors, flow, file, biom, phylip, column, summary, fasta, name, group, list, taxonomy, constaxonomy, contigsreport, qfile, accnos, rabund, sabund, design, order, tree, shared, ordergroup, count, current, relabund, sff, oligos, clear, seed, inputdir, and outputdir. Using 12 processors. [ERROR]: did not complete set.current. mothur > set.current(fasta=180802_pratima.files.trim.contigs.fasta, group=180802_pratima.files.contigs.groups) Using 12 processors. Current files saved by mothur: fasta=180802_pratima.files.trim.contigs.fasta group=180802_pratima.files.contigs.groups processors=12 summary=180802_pratima.files.trim.contigs.pcr.summary Output File Names: current_files.summary mothur > summary.seqs(fasta=current) Using 180802_pratima.files.trim.contigs.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 246 246 0 3 1 2.5%-tile: 1 367 367 0 4 99316 25%-tile: 1 371 371 0 4 993154 Median: 1 373 373 0 5 1986307 75%-tile: 1 374 374 0 6 2979460 97.5%-tile: 1 375 375 5 8 3873298 Maximum: 1 500 500 59 249 3972613 Mean: 1 372 372 0 5 # of Seqs: 3972613 It took 32 secs to summarize 3972613 sequences. Output File Names: 180802_pratima.files.trim.contigs.summary mothur > screen.seqs(fasta=current, group=current, maxambig=0, maxlength=375, minlength=367, maxhomop=8) Using 180802_pratima.files.trim.contigs.fasta as input file for the fasta parameter. Using 180802_pratima.files.contigs.groups as input file for the group parameter. Using 12 processors. It took 16 secs to screen 3972613 sequences, removed 632547. /******************************************/ Running command: remove.seqs(accnos=180802_pratima.files.trim.contigs.bad.accnos, group=180802_pratima.files.contigs.groups) Removed 632547 sequences from your group file. Output File Names: 180802_pratima.files.contigs.pick.groups /******************************************/ Output File Names: 180802_pratima.files.trim.contigs.bad.accnos 180802_pratima.files.trim.contigs.good.fasta 180802_pratima.files.contigs.good.groups It took 37 secs to screen 3972613 sequences. mothur > get.current() Current RAM usage: 0.633945 Gigabytes. Total Ram: 125.888 Gigabytes. Current files saved by mothur: accnos=180802_pratima.files.trim.contigs.bad.accnos fasta=180802_pratima.files.trim.contigs.good.fasta group=180802_pratima.files.contigs.good.groups processors=12 summary=180802_pratima.files.trim.contigs.summary Current default directory saved by mothur: /home/diddyserver/Desktop/pratima/ Current working directory: /home/diddyserver/Desktop/pratima/ Output File Names: current_files.summary mothur > summary.seqs() Using 180802_pratima.files.trim.contigs.good.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 367 367 0 3 1 2.5%-tile: 1 367 367 0 4 83502 25%-tile: 1 372 372 0 4 835017 Median: 1 373 373 0 5 1670034 75%-tile: 1 374 374 0 6 2505050 97.5%-tile: 1 375 375 0 8 3256565 Maximum: 1 375 375 0 8 3340066 Mean: 1 372 372 0 5 # of Seqs: 3340066 It took 26 secs to summarize 3340066 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.summary mothur > unique.seqs(fasta=current) Using 180802_pratima.files.trim.contigs.good.fasta as input file for the fasta parameter. 3340066 1153159 Output File Names: 180802_pratima.files.trim.contigs.good.names 180802_pratima.files.trim.contigs.good.unique.fasta mothur > count.seqs(name=current, group=current) Using 180802_pratima.files.contigs.good.groups as input file for the group parameter. Using 180802_pratima.files.trim.contigs.good.names as input file for the name parameter. It took 50 secs to create a table for 3340066 sequences. Total number of sequences: 3340066 Output File Names: 180802_pratima.files.trim.contigs.good.count_table mothur > summary.seqs(fasta=current, count=current) Using 180802_pratima.files.trim.contigs.good.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 367 367 0 3 1 2.5%-tile: 1 367 367 0 4 83502 25%-tile: 1 372 372 0 4 835017 Median: 1 373 373 0 5 1670034 75%-tile: 1 374 374 0 6 2505050 97.5%-tile: 1 375 375 0 8 3256565 Maximum: 1 375 375 0 8 3340066 Mean: 1 372 372 0 5 # of unique seqs: 1153159 total # of seqs: 3340066 It took 29 secs to summarize 3340066 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.summary mothur > align.seqs(fasta=ecoli_align_silva.fasta, silva.gold.align) silva.gold.align is not a valid parameter. The valid parameters are: reference, fasta, search, ksize, match, align, mismatch, gapopen, gapextend, processors, flip, threshold, seed, inputdir, and outputdir. Unable to open ecoli_align_silva.fasta. Trying default /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Unable to open /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Trying mothur's executable location /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Unable to open /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. no valid files. Using 12 processors. [ERROR]: The reference parameter is a required for the align.seqs command, aborting. [ERROR]: did not complete align.seqs. mothur > align.seqs(fasta=ecoli_align_silva.fasta, reference=silva.gold.align) Unable to open ecoli_align_silva.fasta. Trying default /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Unable to open /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Trying mothur's executable location /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. Unable to open /home/diddyserver/Desktop/pratima/ecoli_align_silva.fasta. no valid files. Using 12 processors. [ERROR]: did not complete align.seqs. mothur > align.seqs(fasta=ecoli_align_silva.fas, reference=silva.gold.align) Using 12 processors. Reading in the silva.gold.align template sequences... DONE. It took 8 to read 5181 sequences. Aligning sequences from ecoli_align_silva.fas ... It took 0 secs to align 1 sequences. Output File Names: ecoli_align_silva.align ecoli_align_silva.align.report mothur > summary.seqs(fasta=ecoli_align_silva.align) Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 13862 27654 373 0 6 1 2.5%-tile: 13862 27654 373 0 6 1 25%-tile: 13862 27654 373 0 6 1 Median: 13862 27654 373 0 6 1 75%-tile: 13862 27654 373 0 6 1 97.5%-tile: 13862 27654 373 0 6 1 Maximum: 13862 27654 373 0 6 1 Mean: 13862 27654 373 0 6 # of Seqs: 1 It took 0 secs to summarize 1 sequences. Output File Names: ecoli_align_silva.summary mothur > get.current() Current RAM usage: 1.59574 Gigabytes. Total Ram: 125.888 Gigabytes. Current files saved by mothur: accnos=180802_pratima.files.trim.contigs.bad.accnos fasta=ecoli_align_silva.align group=180802_pratima.files.contigs.good.groups name=180802_pratima.files.trim.contigs.good.names count=180802_pratima.files.trim.contigs.good.count_table processors=12 summary=ecoli_align_silva.summary Current default directory saved by mothur: /home/diddyserver/Desktop/pratima/ Current working directory: /home/diddyserver/Desktop/pratima/ Output File Names: current_files.summary mothur > pcr.seqs(fasta=silva.gold.align, start=13862, end=27654, keepdots=F) Using 12 processors. It took 1 secs to screen 5181 sequences. Output File Names: silva.gold.pcr.align silva.gold.bad.accnos mothur > align.seqs(fasta=ecoli_align_silva.fas, reference=silva.nr_v132.align) Using 12 processors. Reading in the silva.nr_v132.align template sequences... DONE. It took 311 to read 213119 sequences. Aligning sequences from ecoli_align_silva.fas ... It took 0 secs to align 1 sequences. Output File Names: ecoli_align_silva.align ecoli_align_silva.align.report mothur > summary.seqs(fasta=ecoli_align_silva.align) Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 13862 27654 373 0 6 1 2.5%-tile: 13862 27654 373 0 6 1 25%-tile: 13862 27654 373 0 6 1 Median: 13862 27654 373 0 6 1 75%-tile: 13862 27654 373 0 6 1 97.5%-tile: 13862 27654 373 0 6 1 Maximum: 13862 27654 373 0 6 1 Mean: 13862 27654 373 0 6 # of Seqs: 1 It took 0 secs to summarize 1 sequences. Output File Names: ecoli_align_silva.summary mothur > pcr.seqs(fasta=silva.nr_v132.align, start=13862, end=27654, keepdots=F) Using 12 processors. It took 34 secs to screen 213119 sequences. Output File Names: silva.nr_v132.pcr.align silva.nr_v132.bad.accnos mothur > get.current() Current RAM usage: 12.5953 Gigabytes. Total Ram: 125.888 Gigabytes. Current files saved by mothur: accnos=silva.nr_v132.bad.accnos fasta=silva.nr_v132.pcr.align group=180802_pratima.files.contigs.good.groups name=180802_pratima.files.trim.contigs.good.names count=180802_pratima.files.trim.contigs.good.count_table processors=12 summary=ecoli_align_silva.summary Current default directory saved by mothur: /home/diddyserver/Desktop/pratima/ Current working directory: /home/diddyserver/Desktop/pratima/ Output File Names: current_files.summary mothur > align.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.fasta, reference=silva.nr_v132.pcr.align) Using 12 processors. Reading in the silva.nr_v132.pcr.align template sequences... DONE. It took 85 to read 213119 sequences. Aligning sequences from 180802_pratima.files.trim.contigs.good.unique.fasta ... It took 35527 secs to align 1153159 sequences. [WARNING]: 1811 of your sequences generated alignments that eliminated too many bases, a list is provided in 180802_pratima.files.trim.contigs.good.unique.flip.accnos. [NOTE]: 862 of your sequences were reversed to produce a better alignment. Output File Names: 180802_pratima.files.trim.contigs.good.unique.align 180802_pratima.files.trim.contigs.good.unique.align.report 180802_pratima.files.trim.contigs.good.unique.flip.accnos mothur > screen.seqs(fasta=current, count=current, start=13862, end=27654) Using 180802_pratima.files.trim.contigs.good.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.align as input file for the fasta parameter. Using 12 processors. It took 48 secs to screen 1153159 sequences, removed 1153159. /******************************************/ Running command: remove.seqs(accnos=180802_pratima.files.trim.contigs.good.unique.bad.accnos, count=180802_pratima.files.trim.contigs.good.count_table) Removing group: Mobile_Feed because all sequences have been removed. Removing group: Mobile_Inlet because all sequences have been removed. Removing group: Mobile_Tank because all sequences have been removed. Removing group: Mobile_pooled1 because all sequences have been removed. Removing group: Mobile_pooled2 because all sequences have been removed. Removing group: Mobile_pooled3 because all sequences have been removed. Removing group: Promega_Inlet because all sequences have been removed. Removing group: Promega_feed because all sequences have been removed. Removing group: Promega_pooled1 because all sequences have been removed. Removing group: Promega_pooled2 because all sequences have been removed. Removing group: Promega_pooled3 because all sequences have been removed. Removing group: Promega_tank because all sequences have been removed. Removing group: Qiagen_Blood_pooled1 because all sequences have been removed. Removing group: Qiagen_Blood_pooled2 because all sequences have been removed. Removing group: Qiagen_Blood_pooled3 because all sequences have been removed. Removing group: Qiagen_stool_pooled1 because all sequences have been removed. Removing group: Qiagen_stool_pooled2 because all sequences have been removed. Removing group: Qiagen_stool_pooled3 because all sequences have been removed. Removing group: fast1 because all sequences have been removed. Removing group: fast10 because all sequences have been removed. Removing group: fast11 because all sequences have been removed. Removing group: fast12 because all sequences have been removed. Removing group: fast13 because all sequences have been removed. Removing group: fast14 because all sequences have been removed. Removing group: fast15 because all sequences have been removed. Removing group: fast16 because all sequences have been removed. Removing group: fast17 because all sequences have been removed. Removing group: fast18 because all sequences have been removed. Removing group: fast19 because all sequences have been removed. Removing group: fast2 because all sequences have been removed. Removing group: fast20 because all sequences have been removed. Removing group: fast21 because all sequences have been removed. Removing group: fast22 because all sequences have been removed. Removing group: fast23 because all sequences have been removed. Removing group: fast24 because all sequences have been removed. Removing group: fast3 because all sequences have been removed. Removing group: fast4 because all sequences have been removed. Removing group: fast5 because all sequences have been removed. Removing group: fast6 because all sequences have been removed. Removing group: fast7 because all sequences have been removed. Removing group: fast8 because all sequences have been removed. Removing group: fast9 because all sequences have been removed. Removing group: phenol because all sequences have been removed. Removing group: slow1 because all sequences have been removed. Removing group: slow10 because all sequences have been removed. Removing group: slow11 because all sequences have been removed. Removing group: slow12 because all sequences have been removed. Removing group: slow13 because all sequences have been removed. Removing group: slow14 because all sequences have been removed. Removing group: slow15 because all sequences have been removed. Removing group: slow16 because all sequences have been removed. Removing group: slow17 because all sequences have been removed. Removing group: slow18 because all sequences have been removed. Removing group: slow19 because all sequences have been removed. Removing group: slow2 because all sequences have been removed. Removing group: slow20 because all sequences have been removed. Removing group: slow21 because all sequences have been removed. Removing group: slow3 because all sequences have been removed. Removing group: slow4 because all sequences have been removed. Removing group: slow5 because all sequences have been removed. Removing group: slow6 because all sequences have been removed. Removing group: slow7 because all sequences have been removed. Removing group: slow8 because all sequences have been removed. Removing group: slow9 because all sequences have been removed. Your file contains only sequences from the .accnos file. Removed 3340066 sequences from your count file. Output File Names: 180802_pratima.files.trim.contigs.good.pick.count_table /******************************************/ Output File Names: 180802_pratima.files.trim.contigs.good.unique.bad.accnos 180802_pratima.files.trim.contigs.good.unique.good.align 180802_pratima.files.trim.contigs.good.good.count_table It took 84 secs to screen 1153159 sequences. mothur > summary.seqs(count=180802_pratima.files.trim.contigs.good.count_table, fasta=180802_pratima.files.trim.contigs.good.unique.align) Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 8 1 0 1 1 2.5%-tile: 8 13792 367 0 4 83502 25%-tile: 8 13792 371 0 4 835017 Median: 8 13792 372 0 5 1670034 75%-tile: 8 13792 373 0 6 2505050 97.5%-tile: 8 13792 374 0 8 3256565 Maximum: 13792 13792 375 0 8 3340066 Mean: 24 13789 371 0 5 # of unique seqs: 1153159 total # of seqs: 3340066 It took 68 secs to summarize 3340066 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.summary mothur > screen.seqs(fasta=current, count=current, start=8, end=13792) Using 180802_pratima.files.trim.contigs.good.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.align as input file for the fasta parameter. Using 12 processors. It took 50 secs to screen 1153159 sequences, removed 10233. /******************************************/ Running command: remove.seqs(accnos=180802_pratima.files.trim.contigs.good.unique.bad.accnos, count=180802_pratima.files.trim.contigs.good.count_table) Removed 25438 sequences from your count file. Output File Names: 180802_pratima.files.trim.contigs.good.pick.count_table /******************************************/ Output File Names: 180802_pratima.files.trim.contigs.good.unique.bad.accnos 180802_pratima.files.trim.contigs.good.unique.good.align 180802_pratima.files.trim.contigs.good.good.count_table It took 143 secs to screen 1153159 sequences. mothur > summary.seqs(fasta=current, count=current) Using 180802_pratima.files.trim.contigs.good.good.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.align as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 13792 362 0 3 1 2.5%-tile: 8 13792 367 0 4 82866 25%-tile: 8 13792 371 0 4 828658 Median: 8 13792 372 0 5 1657315 75%-tile: 8 13792 373 0 6 2485972 97.5%-tile: 8 13792 374 0 8 3231763 Maximum: 8 13792 375 0 8 3314628 Mean: 7 13792 371 0 5 # of unique seqs: 1142926 total # of seqs: 3314628 It took 70 secs to summarize 3314628 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.summary mothur > filter.seqs(fasta=current, vertical=T, trump=.) Using 180802_pratima.files.trim.contigs.good.unique.good.align as input file for the fasta parameter. Using 12 processors. Creating Filter... It took 92 secs to create filter for 1142926 sequences. Running Filter... It took 50 secs to filter 1142926 sequences. Length of filtered alignment: 926 Number of columns removed: 12866 Length of the original alignment: 13792 Number of sequences used to construct filter: 1142926 Output File Names: 180802_pratima.filter 180802_pratima.files.trim.contigs.good.unique.good.filter.fasta mothur > unique.seqs(fasta=current, count=current) Using 180802_pratima.files.trim.contigs.good.good.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.fasta as input file for the fasta parameter. 1142926 1138404 Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.count_table 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.fasta mothur > summary.seqs(fasta=current, count=current) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 926 362 0 3 1 2.5%-tile: 1 926 367 0 4 82866 25%-tile: 1 926 371 0 4 828658 Median: 1 926 372 0 5 1657315 75%-tile: 1 926 373 0 6 2485972 97.5%-tile: 1 926 374 0 8 3231763 Maximum: 1 926 375 0 8 3314628 Mean: 1 926 371 0 5 # of unique seqs: 1138404 total # of seqs: 3314628 It took 32 secs to summarize 3314628 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.summary mothur > pre.cluster(fasta=current, count=current, diffs=3) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.fasta as input file for the fasta parameter. Using 12 processors. Processing group fast20: Processing group Qiagen_stool_pooled1: Processing group fast11: Processing group Mobile_pooled3: Processing group slow18: Processing group fast16: Processing group fast8: Processing group fast3: Processing group Promega_pooled3: Processing group slow4: Processing group slow12: fast11 9985 1828 8157 Total number of sequences before pre.cluster was 9985. pre.cluster removed 8157 sequences. It took 2 secs to cluster 8157 sequences. Processing group fast12: Qiagen_stool_pooled1 8916 2081 6835 Total number of sequences before pre.cluster was 8916. pre.cluster removed 6835 sequences. It took 3 secs to cluster 6835 sequences. Processing group Qiagen_stool_pooled2: slow12 7858 1817 6041 Total number of sequences before pre.cluster was 7858. pre.cluster removed 6041 sequences. It took 2 secs to cluster 6041 sequences. Processing group slow13: Qiagen_stool_pooled2 5892 1270 4622 Total number of sequences before pre.cluster was 5892. pre.cluster removed 4622 sequences. It took 1 secs to cluster 4622 sequences. Processing group Qiagen_stool_pooled3: fast16 18775 3484 15291 Total number of sequences before pre.cluster was 18775. pre.cluster removed 15291 sequences. It took 7 secs to cluster 15291 sequences. Processing group fast17: slow18 18036 3890 14146 Total number of sequences before pre.cluster was 18036. pre.cluster removed 14146 sequences. It took 10 secs to cluster 14146 sequences. Processing group slow19: slow13 15949 3714 12235 Total number of sequences before pre.cluster was 15949. pre.cluster removed 12235 sequences. It took 7 secs to cluster 12235 sequences. Processing group slow14: fast20 20997 4197 16800 Total number of sequences before pre.cluster was 20997. pre.cluster removed 16800 sequences. It took 12 secs to cluster 16800 sequences. Processing group fast21: slow14 10285 2371 7914 Total number of sequences before pre.cluster was 10285. pre.cluster removed 7914 sequences. It took 4 secs to cluster 7914 sequences. Processing group slow15: fast17 17732 3949 13783 Total number of sequences before pre.cluster was 17732. pre.cluster removed 13783 sequences. It took 9 secs to cluster 13783 sequences. Processing group fast18: Processing group Mobile_Feed: Mobile_pooled3 27559 5797 21762 Total number of sequences before pre.cluster was 27559. pre.cluster removed 21762 sequences. It took 20 secs to cluster 21762 sequences. Processing group Promega_Inlet: fast18 15417 2746 12671 Total number of sequences before pre.cluster was 15417. pre.cluster removed 12671 sequences. It took 4 secs to cluster 12671 sequences. Processing group fast19: Qiagen_stool_pooled3 21650 5548 16102 Total number of sequences before pre.cluster was 21650. pre.cluster removed 16102 sequences. It took 21 secs to cluster 16102 sequences. Processing group fast1: slow4 20508 5696 14812 Total number of sequences before pre.cluster was 20508. pre.cluster removed 14812 sequences. fast8 23126 5783 17343 Total number of sequences before pre.cluster was 23126. pre.cluster removed 17343 sequences. It took 23 secs to cluster 14812 sequences. Processing group slow5: It took 24 secs to cluster 17343 sequences. Processing group fast9: slow15 19463 4920 14543 Total number of sequences before pre.cluster was 19463. pre.cluster removed 14543 sequences. It took 16 secs to cluster 14543 sequences. Processing group slow16: fast19 18543 3968 14575 Total number of sequences before pre.cluster was 18543. pre.cluster removed 14575 sequences. It took 11 secs to cluster 14575 sequences. Processing group fast2: fast21 22295 5296 16999 Total number of sequences before pre.cluster was 22295. pre.cluster removed 16999 sequences. It took 23 secs to cluster 16999 sequences. Processing group fast22: fast9 23350 4900 18450 Total number of sequences before pre.cluster was 23350. pre.cluster removed 18450 sequences. It took 16 secs to cluster 18450 sequences. Processing group phenol: Promega_pooled3 21858 7695 14163 Total number of sequences before pre.cluster was 21858. pre.cluster removed 14163 sequences. It took 40 secs to cluster 14163 sequences. Processing group Promega_tank: fast12 26798 7262 19536 Total number of sequences before pre.cluster was 26798. pre.cluster removed 19536 sequences. It took 42 secs to cluster 19536 sequences. Processing group fast13: fast13 7601 1746 5855 Total number of sequences before pre.cluster was 7601. pre.cluster removed 5855 sequences. It took 2 secs to cluster 5855 sequences. Processing group fast14: slow16 25745 4887 20858 Total number of sequences before pre.cluster was 25745. pre.cluster removed 20858 sequences. It took 17 secs to cluster 20858 sequences. Processing group slow17: fast3 27732 8572 19160 Total number of sequences before pre.cluster was 27732. pre.cluster removed 19160 sequences. It took 54 secs to cluster 19160 sequences. Processing group fast4: Promega_Inlet 26942 6638 20304 Total number of sequences before pre.cluster was 26942. pre.cluster removed 20304 sequences. It took 35 secs to cluster 20304 sequences. Processing group Promega_feed: Promega_tank 17347 4465 12882 Total number of sequences before pre.cluster was 17347. pre.cluster removed 12882 sequences. It took 15 secs to cluster 12882 sequences. Processing group Qiagen_Blood_pooled1: Qiagen_Blood_pooled1 14680 2913 11767 Total number of sequences before pre.cluster was 14680. pre.cluster removed 11767 sequences. It took 5 secs to cluster 11767 sequences. Processing group Qiagen_Blood_pooled2: Qiagen_Blood_pooled2 8035 1277 6758 Total number of sequences before pre.cluster was 8035. pre.cluster removed 6758 sequences. It took 2 secs to cluster 6758 sequences. Processing group Qiagen_Blood_pooled3: slow17 22335 5002 17333 Total number of sequences before pre.cluster was 22335. pre.cluster removed 17333 sequences. It took 17 secs to cluster 17333 sequences. fast22 26430 6272 20158 Total number of sequences before pre.cluster was 26430. pre.cluster removed 20158 sequences. It took 31 secs to cluster 20158 sequences. Processing group fast23: fast14 25167 5635 19532 Total number of sequences before pre.cluster was 25167. pre.cluster removed 19532 sequences. It took 23 secs to cluster 19532 sequences. Processing group fast15: Mobile_Feed 22656 6305 16351 Total number of sequences before pre.cluster was 22656. pre.cluster removed 16351 sequences. It took 52 secs to cluster 16351 sequences. Processing group Mobile_Inlet: fast15 10245 2434 7811 Total number of sequences before pre.cluster was 10245. pre.cluster removed 7811 sequences. It took 3 secs to cluster 7811 sequences. Qiagen_Blood_pooled3 21734 4659 17075 Total number of sequences before pre.cluster was 21734. pre.cluster removed 17075 sequences. It took 12 secs to cluster 17075 sequences. slow5 28354 8356 19998 Total number of sequences before pre.cluster was 28354. pre.cluster removed 19998 sequences. It took 53 secs to cluster 19998 sequences. Processing group slow6: Promega_feed 18689 6032 12657 Total number of sequences before pre.cluster was 18689. pre.cluster removed 12657 sequences. It took 25 secs to cluster 12657 sequences. Processing group Promega_pooled1: fast23 22320 5538 16782 Total number of sequences before pre.cluster was 22320. pre.cluster removed 16782 sequences. It took 20 secs to cluster 16782 sequences. Processing group fast24: fast4 22651 6958 15693 Total number of sequences before pre.cluster was 22651. pre.cluster removed 15693 sequences. It took 31 secs to cluster 15693 sequences. Processing group fast5: fast24 16010 3704 12306 Total number of sequences before pre.cluster was 16010. pre.cluster removed 12306 sequences. It took 7 secs to cluster 12306 sequences. fast2 37094 9882 27212 Total number of sequences before pre.cluster was 37094. pre.cluster removed 27212 sequences. It took 68 secs to cluster 27212 sequences. Mobile_Inlet 30458 5626 24832 Total number of sequences before pre.cluster was 30458. pre.cluster removed 24832 sequences. It took 32 secs to cluster 24832 sequences. Processing group Mobile_Tank: fast5 22228 5665 16563 Total number of sequences before pre.cluster was 22228. pre.cluster removed 16563 sequences. It took 18 secs to cluster 16563 sequences. Processing group fast6: fast6 76 46 30 Total number of sequences before pre.cluster was 76. pre.cluster removed 30 sequences. It took 0 secs to cluster 30 sequences. Processing group fast7: slow6 26545 7337 19208 Total number of sequences before pre.cluster was 26545. pre.cluster removed 19208 sequences. It took 36 secs to cluster 19208 sequences. Processing group slow7: phenol 43091 10771 32320 Total number of sequences before pre.cluster was 43091. pre.cluster removed 32320 sequences. It took 84 secs to cluster 32320 sequences. Processing group slow1: Mobile_Tank 20832 5263 15569 Total number of sequences before pre.cluster was 20832. pre.cluster removed 15569 sequences. It took 26 secs to cluster 15569 sequences. Processing group Mobile_pooled1: slow7 20339 5343 14996 Total number of sequences before pre.cluster was 20339. pre.cluster removed 14996 sequences. It took 16 secs to cluster 14996 sequences. Processing group slow8: slow8 3406 731 2675 Total number of sequences before pre.cluster was 3406. pre.cluster removed 2675 sequences. It took 1 secs to cluster 2675 sequences. Processing group slow9: slow9 10654 1950 8704 Total number of sequences before pre.cluster was 10654. pre.cluster removed 8704 sequences. It took 2 secs to cluster 8704 sequences. fast7 34838 8819 26019 Total number of sequences before pre.cluster was 34838. pre.cluster removed 26019 sequences. It took 49 secs to cluster 26019 sequences. slow19 59753 14635 45118 Total number of sequences before pre.cluster was 59753. pre.cluster removed 45118 sequences. It took 157 secs to cluster 45118 sequences. Processing group slow2: slow1 32417 9049 23368 Total number of sequences before pre.cluster was 32417. pre.cluster removed 23368 sequences. It took 46 secs to cluster 23368 sequences. Processing group slow10: slow10 305 161 144 Total number of sequences before pre.cluster was 305. pre.cluster removed 144 sequences. It took 1 secs to cluster 144 sequences. Processing group slow11: slow2 18744 4506 14238 Total number of sequences before pre.cluster was 18744. pre.cluster removed 14238 sequences. It took 10 secs to cluster 14238 sequences. Processing group slow20: slow11 16135 3747 12388 Total number of sequences before pre.cluster was 16135. pre.cluster removed 12388 sequences. It took 6 secs to cluster 12388 sequences. Promega_pooled1 47135 12201 34934 Total number of sequences before pre.cluster was 47135. pre.cluster removed 34934 sequences. It took 101 secs to cluster 34934 sequences. Processing group Promega_pooled2: Mobile_pooled1 29889 8096 21793 Total number of sequences before pre.cluster was 29889. pre.cluster removed 21793 sequences. It took 54 secs to cluster 21793 sequences. Processing group Mobile_pooled2: fast1 55032 15459 39573 Total number of sequences before pre.cluster was 55032. pre.cluster removed 39573 sequences. It took 160 secs to cluster 39573 sequences. Processing group fast10: Mobile_pooled2 8848 1901 6947 Total number of sequences before pre.cluster was 8848. pre.cluster removed 6947 sequences. It took 2 secs to cluster 6947 sequences. slow20 20386 4301 16085 Total number of sequences before pre.cluster was 20386. pre.cluster removed 16085 sequences. It took 9 secs to cluster 16085 sequences. Processing group slow21: Promega_pooled2 24347 6698 17649 Total number of sequences before pre.cluster was 24347. pre.cluster removed 17649 sequences. It took 18 secs to cluster 17649 sequences. slow21 26326 6123 20203 Total number of sequences before pre.cluster was 26326. pre.cluster removed 20203 sequences. It took 18 secs to cluster 20203 sequences. Processing group slow3: slow3 23849 5653 18196 Total number of sequences before pre.cluster was 23849. pre.cluster removed 18196 sequences. It took 12 secs to cluster 18196 sequences. fast10 64612 13048 51564 Total number of sequences before pre.cluster was 64612. pre.cluster removed 51564 sequences. It took 66 secs to cluster 51564 sequences. It took 380 secs to run pre.cluster. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fasta 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.count_table 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_Feed.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_Inlet.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_Tank.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_pooled1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_pooled2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Mobile_pooled3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_Inlet.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_feed.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_pooled1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_pooled2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_pooled3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Promega_tank.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_Blood_pooled1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_Blood_pooled2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_Blood_pooled3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_stool_pooled1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_stool_pooled2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.Qiagen_stool_pooled3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast10.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast11.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast12.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast13.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast14.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast15.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast16.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast17.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast18.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast19.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast20.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast21.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast22.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast23.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast24.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast4.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast5.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast6.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast7.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast8.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fast9.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.phenol.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow1.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow10.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow11.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow12.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow13.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow14.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow15.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow16.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow17.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow18.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow19.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow2.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow20.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow21.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow3.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow4.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow5.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow6.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow7.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow8.map 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.slow9.map mothur > chimera.vsearch(fasta=current, count=current, dereplicate=t) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter. Using 12 processors. Checking sequences from 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fasta ... It took 16 secs to check 6305 sequences from group Mobile_Feed. It took 13 secs to check 5626 sequences from group Mobile_Inlet. It took 13 secs to check 5263 sequences from group Mobile_Tank. It took 21 secs to check 8096 sequences from group Mobile_pooled1. It took 4 secs to check 1901 sequences from group Mobile_pooled2. It took 14 secs to check 5797 sequences from group Mobile_pooled3. It took 17 secs to check 6638 sequences from group Promega_Inlet. It took 14 secs to check 6032 sequences from group Promega_feed. It took 32 secs to check 12201 sequences from group Promega_pooled1. It took 16 secs to check 6698 sequences from group Promega_pooled2. It took 19 secs to check 7695 sequences from group Promega_pooled3. It took 11 secs to check 4465 sequences from group Promega_tank. It took 7 secs to check 2913 sequences from group Qiagen_Blood_pooled1. It took 3 secs to check 1277 sequences from group Qiagen_Blood_pooled2. It took 11 secs to check 4659 sequences from group Qiagen_Blood_pooled3. It took 5 secs to check 2081 sequences from group Qiagen_stool_pooled1. It took 2 secs to check 1270 sequences from group Qiagen_stool_pooled2. It took 14 secs to check 5548 sequences from group Qiagen_stool_pooled3. It took 41 secs to check 15459 sequences from group fast1. It took 34 secs to check 13048 sequences from group fast10. It took 4 secs to check 1828 sequences from group fast11. It took 19 secs to check 7262 sequences from group fast12. It took 4 secs to check 1746 sequences from group fast13. It took 14 secs to check 5635 sequences from group fast14. It took 5 secs to check 2434 sequences from group fast15. It took 8 secs to check 3484 sequences from group fast16. It took 10 secs to check 3949 sequences from group fast17. It took 6 secs to check 2746 sequences from group fast18. It took 9 secs to check 3968 sequences from group fast19. It took 25 secs to check 9882 sequences from group fast2. It took 10 secs to check 4197 sequences from group fast20. It took 13 secs to check 5296 sequences from group fast21. It took 16 secs to check 6272 sequences from group fast22. It took 13 secs to check 5538 sequences from group fast23. It took 9 secs to check 3704 sequences from group fast24. It took 21 secs to check 8572 sequences from group fast3. It took 17 secs to check 6958 sequences from group fast4. It took 14 secs to check 5665 sequences from group fast5. It took 0 secs to check 46 sequences from group fast6. It took 22 secs to check 8819 sequences from group fast7. It took 14 secs to check 5783 sequences from group fast8. It took 12 secs to check 4900 sequences from group fast9. It took 27 secs to check 10771 sequences from group phenol. It took 23 secs to check 9049 sequences from group slow1. It took 0 secs to check 161 sequences from group slow10. It took 9 secs to check 3747 sequences from group slow11. It took 4 secs to check 1817 sequences from group slow12. It took 9 secs to check 3714 sequences from group slow13. It took 5 secs to check 2371 sequences from group slow14. It took 12 secs to check 4920 sequences from group slow15. It took 12 secs to check 4887 sequences from group slow16. It took 11 secs to check 5002 sequences from group slow17. It took 10 secs to check 3890 sequences from group slow18. It took 39 secs to check 14635 sequences from group slow19. It took 11 secs to check 4506 sequences from group slow2. It took 10 secs to check 4301 sequences from group slow20. It took 15 secs to check 6123 sequences from group slow21. It took 14 secs to check 5653 sequences from group slow3. It took 14 secs to check 5696 sequences from group slow4. It took 20 secs to check 8356 sequences from group slow5. It took 18 secs to check 7337 sequences from group slow6. It took 13 secs to check 5343 sequences from group slow7. It took 2 secs to check 731 sequences from group slow8. It took 5 secs to check 1950 sequences from group slow9. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos mothur > remove.seqs(fasta=current, accnos=current) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos as input file for the accnos parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter. [WARNING]: This command can take a namefile and you did not provide one. The current namefile is 180802_pratima.files.trim.contigs.good.names which seems to match 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.fasta. Removed 65109 sequences from your fasta file. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta mothur > summary.seqs(fasta=current, count=current) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter. Using 12 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 926 363 0 3 1 2.5%-tile: 1 926 367 0 4 78773 25%-tile: 1 926 371 0 4 787730 Median: 1 926 372 0 5 1575460 75%-tile: 1 926 373 0 6 2363190 97.5%-tile: 1 926 374 0 8 3072147 Maximum: 1 926 375 0 8 3150919 Mean: 1 926 371 0 5 # of unique seqs: 269200 total # of seqs: 3150919 It took 7 secs to summarize 3150919 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.summary mothur > classify.seqs(fasta=current, count=current, reference=silva.nr_v132.align, taxonomy=silva.nr_v132.tax) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter. Using 12 processors. Generating search database... DONE. It took 331 seconds generate search database. Reading in the silva.nr_v132.tax taxonomy... DONE. Calculating template taxonomy tree... DONE. Calculating template probabilities... DONE. It took 607 seconds get probabilities. Classifying sequences from 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta ... [WARNING]: M03064_15_000000000-BNFWC_1_1111_16414_17555 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2102_29245_16679 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2103_6691_6103 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2111_3327_21419 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2114_3506_21431 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2103_29246_14096 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2109_29193_18035 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1113_8382_26415 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1108_29202_18113 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1105_22033_26402 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2113_8654_26540 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1113_26427_16599 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2106_7337_26533 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1111_7504_26413 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1105_21889_26405 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1105_15846_12772 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1114_7272_26404 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1114_24053_26408 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1107_29214_13930 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1111_22182_26339 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2110_8555_22653 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1101_22356_11689 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2109_29199_16418 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2107_11024_5474 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1111_5046_7625 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2112_29168_13444 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2103_27065_13722 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2108_14999_12445 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1111_22184_26320 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1112_14163_10231 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2112_29170_13480 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2109_17842_19104 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1106_16666_6644 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1109_26831_22010 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_1110_23474_18342 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. [WARNING]: M03064_15_000000000-BNFWC_1_2108_6177_5800 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences. It took 3095 secs to classify 269200 sequences. It took 3095 secs to classify 269200 sequences. It took 21 secs to create the summary file for 269200 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.taxonomy 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.tax.summary mothur > remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.taxonomy as input file for the taxonomy parameter. [NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table mothur > summary.tax(taxonomy=current, count=current) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy as input file for the taxonomy parameter. It took 13 secs to create the summary file for 2524985 sequences. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.tax.summary mothur > cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.03) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta as input file for the fasta parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy as input file for the taxonomy parameter. Using 12 processors. Splitting the file... /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.0.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff quitting command... It took 125 secs to find distances for 19888 sequences. 11162637 distances below cutoff 0.03. /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.1.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.3.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.4.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.8.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.10.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.11.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.13.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.14.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.15.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.16.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.17.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.18.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.19.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.20.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.21.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.22.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.23.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.25.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.26.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.27.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.28.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.30.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.31.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.32.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.33.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.34.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.35.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.37.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.38.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.39.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.41.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.42.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.43.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.45.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.46.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.47.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.48.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.49.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.50.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.52.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.53.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.54.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.55.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.57.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.58.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.59.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.60.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.61.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.62.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.65.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.66.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.67.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.68.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.69.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.70.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.71.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.73.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.74.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.75.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.76.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.79.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.80.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.81.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.83.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.84.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.85.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.86.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.87.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.88.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.89.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.91.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.92.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.95.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.96.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.97.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.99.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.100.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.102.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.104.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.105.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.106.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.109.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.110.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.113.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.117.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.119.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.120.temp, processors=12, cutoff=0.03) Linux version Using ReadLine Using Boost Running 64Bit Version mothur v.1.40.2 Last updated: 4/23/2018 by Patrick D. Schloss Department of Microbiology & Immunology University of Michigan http://www.mothur.org When using, please cite: Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. Distributed under the GNU General Public License Type 'help()' for information on the commands that are available For questions and analysis support, please visit our forum at https://www.mothur.org/forum Type 'quit()' to exit program Interactive Mode mothur > set.current(processors=12, fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, taxonomy=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy) Using 12 processors. Current files saved by mothur: fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta taxonomy=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy count=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table processors=12 Output File Names: current_files.summary mothur > cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.03, method=opti) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta as input file for the fasta parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy as input file for the taxonomy parameter. Using 12 processors. Splitting the file... /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.0.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 294 secs to find distances for 19888 sequences. 25330065 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.0.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.1.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 574 secs to find distances for 28033 sequences. 17113955 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.1.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 8 secs to find distances for 3165 sequences. 373895 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.3.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 623 secs to find distances for 29242 sequences. 15422187 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.3.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.4.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1091 secs to find distances for 37957 sequences. 190926311 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.4.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 1144 sequences. 188115 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 388 secs to find distances for 22805 sequences. 16171544 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 6 secs to find distances for 2614 sequences. 1494065 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.8.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 3 secs to find distances for 1906 sequences. 75626 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.8.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 551 secs to find distances for 26332 sequences. 168532192 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.10.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 17 secs to find distances for 4543 sequences. 2040458 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.10.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.11.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 7 secs to find distances for 2978 sequences. 253431 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.11.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 18 secs to find distances for 4755 sequences. 1047151 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.13.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 17 secs to find distances for 4542 sequences. 1843596 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.13.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.14.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 1112 sequences. 514 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.14.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.15.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 48 secs to find distances for 7987 sequences. 3934666 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.15.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.16.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 13 secs to find distances for 4116 sequences. 1508810 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.16.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.17.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 10 secs to find distances for 3362 sequences. 2047990 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.17.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.18.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 37 secs to find distances for 6825 sequences. 1185848 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.18.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.19.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 363 sequences. 11504 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.19.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.20.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 274 sequences. 6027 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.20.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.21.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 2 secs to find distances for 1399 sequences. 68228 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.21.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.22.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 33 secs to find distances for 6238 sequences. 7219870 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.22.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.23.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 1278 sequences. 335028 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.23.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 13 sequences. 16 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.25.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 597 sequences. 15670 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.25.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.26.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 241 sequences. 20334 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.26.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.27.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 4 secs to find distances for 2156 sequences. 796161 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.27.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.28.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 297 sequences. 3454 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.28.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 498 sequences. 15707 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.30.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 127 sequences. 227 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.30.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.31.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 22 sequences. 15 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.31.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.32.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 20 secs to find distances for 4990 sequences. 4907299 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.32.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.33.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 67 sequences. 317 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.33.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.34.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 90 sequences. 590 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.34.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.35.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 90 sequences. 939 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.35.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 14 sequences. 29 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.37.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 82 sequences. 1215 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.37.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.38.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 482 sequences. 25059 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.38.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.39.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 45 sequences. 88 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.39.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 88 sequences. 1232 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.41.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 7 sequences. 7 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.41.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.42.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 11 sequences. 26 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.42.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.43.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 345 sequences. 9724 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.43.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 234 sequences. 332 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.45.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 99 sequences. 61 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.45.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.46.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 308 sequences. 5499 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.46.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.47.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 46 sequences. 190 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.47.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.48.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 282 sequences. 13547 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.48.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.49.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 11 sequences. 39 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.49.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.50.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 54 sequences. 342 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.50.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 5 sequences. 10 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.52.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 12 sequences. 36 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.52.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.53.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 216 sequences. 1678 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.53.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.54.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 1 secs to find distances for 346 sequences. 14031 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.54.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.55.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 144 sequences. 4629 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.55.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 216 sequences. 1963 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.57.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 41 sequences. 328 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.57.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.58.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 200 sequences. 8413 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.58.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.59.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 522 sequences. 9428 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.59.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.60.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 10 sequences. 14 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.60.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.61.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 10 sequences. 10 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.61.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.62.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 81 sequences. 83 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.62.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 8 sequences. 9 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 5 sequences. 10 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.65.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 10 sequences. 29 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.65.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.66.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 14 sequences. 42 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.66.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.67.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 18 sequences. 40 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.67.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.68.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 28 sequences. 232 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.68.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.69.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 114 sequences. 773 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.69.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.70.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 142 sequences. 1097 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.70.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.71.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 12 sequences. 54 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.71.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 28 sequences. 104 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.73.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 15 sequences. 27 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.73.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.74.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 41 sequences. 268 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.74.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.75.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 12 sequences. 27 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.75.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.76.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 58 sequences. 282 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.76.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 40 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 17 sequences. 16 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.79.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 45 sequences. 143 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.79.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.80.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 83 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.80.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.81.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 59 sequences. 621 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.81.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 9 sequences. 5 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.83.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 15 sequences. 24 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.83.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.84.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 13 sequences. 12 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.84.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.85.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 21 sequences. 11 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.85.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.86.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 9 sequences. 13 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.86.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.87.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 14 sequences. 44 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.87.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.88.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 6 sequences. 14 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.88.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.89.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 48 sequences. 249 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.89.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 11 sequences. 30 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.91.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 4 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.91.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.92.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 8 sequences. 8 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.92.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.95.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 22 sequences. 170 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.95.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.96.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 24 sequences. 22 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.96.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.97.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 21 sequences. 82 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.97.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.99.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 7 sequences. 10 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.99.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.100.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 11 sequences. 23 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.100.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 7 sequences. 5 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.102.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 10 sequences. 7 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.102.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.104.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 48 sequences. 382 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.104.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.105.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 17 sequences. 28 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.105.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.106.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 24 sequences. 187 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.106.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 4 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 18 sequences. 17 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.109.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 10 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.109.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.110.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 13 sequences. 72 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.110.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.113.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 12 sequences. 20 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.113.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 8 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.117.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.117.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.117.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.119.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 4 sequences. 2 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.119.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.120.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 16 sequences. 27 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.120.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.121.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 4 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.121.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.121.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.122.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 5 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.122.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.123.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.123.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.123.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.124.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 8 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.124.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.125.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 6 sequences. 6 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.125.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.126.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.126.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.126.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.127.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 6 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.127.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.128.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 5 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.128.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.129.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.129.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.129.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.130.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 5 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.130.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.130.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.131.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.131.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.132.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.132.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.133.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.133.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.134.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.134.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.134.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.135.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.135.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.136.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 0 distances below cutoff 0.03. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.136.dist is blank. This can result if there are no distances below your cutoff. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.136.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.138.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.138.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.139.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 6 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.139.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.140.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.140.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.141.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 4 sequences. 2 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.141.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.142.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.142.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.143.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.143.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.144.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.144.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.145.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 6 sequences. 15 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.145.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.146.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.146.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.147.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.147.dist /******************************************/ Running command: dist.seqs(fasta=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.148.temp, processors=12, cutoff=0.03) Using 12 processors. /******************************************/ Sequence Time Num_Dists_Below_Cutoff It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.03. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.148.dist It took 4017 seconds to split the distance file. 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.128.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.127.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.122.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.140.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.132.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1769 0 1 0 1710 0 1 0 1652 0 1 0 0 0 1 1 1 0 0 **0.999435 0.999395 0.999416 1 1 1 0.999435 0.999395 0.999416 0 0 0 0 0 0 0 1652 0 1 0 1829 0 1 0 0 1 1 0 0 0.999454 0.999395 1 1 0.999454 0.999395 0 0 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1829 0 1 0 1 0 0.999454 1 0.999454 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1890 0 1 0 1 0 0.999471 1 0.999471 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 4559 0 1 0 1 0 0.999781 1 0.999781 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.142.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.143.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.144.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.138.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.133.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.146.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.dist 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.147.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 4 1948 0 1 0 0.8 1 0.999395 1 1 0.999487 0.999395 1 0 0.999488 0 894198 as 0.888889 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.141.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.131.dist 0 1652 0 1 0 1 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.999395 6 2007 0 3 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.dist 0 1708 0 3 0 1 0 0.998247 1 0 1710 0 1 0 1 0 1 0.999416 1 0.999395 0.999416 0 0 0 0 0.666667 1 1 0.998507 1 0.998512 0.815887 0.8 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.139.dist 0.998247 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 0.999395 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.dist 0.999395 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1820 0 10 0 1 0 0.994536 1 0.994536 0 0 1 0 0 0 2010 0 6 0 1 0 0.998247 0 0.997024 0 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1888 0 3 0 1 0 0.998414 1 0.998414 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score .files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.128.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.127.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.122.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.140.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.132.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1769 0 1 0 1710 0 1 0 1652 0 1 0 0 0 1 1 1 0 0 **0.999435 0.999395 0.999416 1 1 1 0.999435 0.999395 0.999416 0 0 0 0 0 0 0 1652 0 1 0 1829 0 1 0 0 1 1 0 0 0.999454 0.999395 1 1 0.999454 0.999395 0 0 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1829 0 1 0 1 0 0.999454 1 0.999454 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1890 0 1 0 1 0 0.999471 1 0.999471 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 4559 0 1 0 1 0 0.999781 1 0.999781 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.142.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.143.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.144.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.138.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.133.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.146.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.dist 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.147.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 4 1948 0 1 0 0.8 1 0.999395 1 1 0.999487 0.999395 1 0 0.999488 0 894198 as 0.888889 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.141.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.131.dist 0 1652 0 1 0 1 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.999395 6 2007 0 3 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.dist 0 1708 0 3 0 1 0 0.998247 1 0 1710 0 1 0 1 0 1 0.999416 1 0.999395 0.999416 0 0 0 0 0.666667 1 1 0.998507 1 0.998512 0.815887 0.8 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.139.dist 0.998247 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 0.999395 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.dist 0.999395 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1820 0 10 0 1 0 0.994536 1 0.994536 0 0 1 0 0 0 2010 0 6 0 1 0 0.998247 0 0.997024 0 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.997024 0 1888 0 3 0 1 0 0.998414 1 0.998414 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score .files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.107.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.116.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.77.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.128.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.103.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.127.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.111.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.122.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.140.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.137.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.132.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1769 0 1 0 1710 0 1 0 1652 0 1 0 0 0 1 1 1 0 0 **0.999435 0.999395 0.999416 1 1 1 0.999435 0.999395 0.999416 0 0 0 0 0 0 0 1652 0 1 0 1829 0 1 0 0 1 1 0 0 0.999454 0.999395 1 1 0.999454 0.999395 0 0 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1829 0 1 0 1 0 0.999454 1 0.999454 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1890 0 1 0 1 0 0.999471 1 0.999471 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 4559 0 1 0 1 0 0.999781 1 0.999781 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.118.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.142.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.143.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.144.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.93.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.98.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.94.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.138.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.133.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.112.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.146.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.101.dist 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 0 1 0 0.999416 1 0.999416 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.63.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.147.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 4 1948 0 1 0 0.8 1 0.999395 1 1 0.999487 0.999395 1 0 0.999488 0 894198 as 0.888889 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.141.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.131.dist 0 1652 0 1 0 1 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.999395 6 2007 0 3 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.64.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.115.dist 0 1708 0 3 0 1 0 0.998247 1 0 1710 0 1 0 1 0 1 0.999416 1 0.999395 0.999416 0 0 0 0 0.666667 1 1 0.998507 1 0.998512 0.815887 0.8 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.139.dist 0.998247 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 0.999395 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.78.dist 0.999395 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1820 0 10 0 1 0 0.994536 1 0.994536 0 0 1 0 0 0 2010 0 6 0 1 0 0.998247 0 0.997024 0 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.114.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.82.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1 0.998247 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.109.dist 13 2612 0 3 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.8125 0 1708 0 3 0 1 2 1768 0 0 0 5 2075 0 0 0.998247 1 1 1 0 0 0 1708 0 3 0 1 1 1 1 1 1 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1 1 0 0.998853 16 2330 0 0 1 1 1 1 1 1 1 1 0 1 0.998858 0.900871 0.896552 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.85.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.65.dist 1 0 0.998247 1 0.998247 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.51.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.80.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.41.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1 6 2139 0 0 1 1 1 1 1 1 0.998247 1 0 1 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.92.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.86.dist 28 2116 0 1 0.965517 1 1 0.999528 1 0.999534 0.982375 0.982456 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 7 1946 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.88.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.39.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.102.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 21 2386 0 8 0.724138 1 1 0.996658 1 0.996687 0.84954 0.84 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 12 2066 1 1 0 1820 0 10 0 1 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.994536 1 0.994536 8 2008 0 0 11 2915 0 0 1 0.923077 1 1 0.999516 1 0.923077 1 0.999516 1 0.923077 1 0.999038 1 0.922593 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.100.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1710 0 1 10 1877 0 4 0.714286 1 1 0.997873 1 0.997885 0.844255 0.833333 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 7 2138 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.120.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.145.dist 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.62.dist 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 16 2188 0 7 0.695652 1 1 0.996811 1 0.996834 0.832727 0.820513 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 27 2527 2 0 1 0.999209 0.931034 1 0.931034 0.999218 0.96452 0.964286 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.108.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.67.dist 75 4954 8 13 0.852273 0.998388 0.903614 0.997383 0.903614 0.995842 0.875467 0.877193 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1876 0 15 0 1 0 0.992068 1 0.992068 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.45.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.73.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 83 9230 3 0 1 0.999675 0.965116 1 0.965116 0.999678 0.982244 0.982249 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 6 9584 1 0 1 0.999896 0.857143 1 0.857143 0.999896 0.925772 0.923077 0.923077 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.42.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.57.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.84.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 12 2334 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.83.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 14 2683 1 3 0.823529 0.999627 0.933333 0.998883 0.933333 0.998519 0.875991 0.875 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 21 2185 0 5 0.807692 1 1 0.997717 1 0.997739 0.897691 0.893617 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.90.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.33.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.87.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 28 2181 0 2 0.933333 1 1 0.999084 1 0.999095 0.965649 0.965517 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 35 2370 1 9 0.795455 0.999578 0.972222 0.996217 0.972222 0.995859 0.877463 0.875 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.72.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 295 7170 16 22 0.930599 0.997773 0.948553 0.996941 0.948553 0.994935 0.936894 0.93949 0 1 0 0.999416 1 0.999416 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 104 3381 1 0 1 0.999704 0.990476 1 0.990476 0.999713 0.99508 0.995215 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.30.dist 41 11870 4 20 0.672131 0.999663 0.911111 0.998318 0.911111 0.997989 0.781632 0.773585 21 2460 1 3 0.875 0.999594 0.954545 0.998782 0.954545 0.99839 0.913112 0.913043 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.66.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.89.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 209 16417 9 18 0.920705 0.999452 0.958716 0.998905 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.958716 1 24 2660 1 16 42 2373 0 0 1 1 1 1 1 1 1 1 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 242 5048 59 7 0.971888 0.988447 0.803987 0.998615 0.803987 0.987677 0.877933 0.88 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.47.dist 0.6 0.998379 0.999624 0.938702 0.96 0.939326 0.994021 0 1 0.96 0.993706 0.756343 0.738462 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.106.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.135.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1708 0 3 0 1 0 0.998247 1 0.998247 0 0 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 309 4321 7 19 0.942073 0.998383 0.977848 0.995622 0.977848 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.125.dist 0.994416 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.956821 0.959627 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 6 1885 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.60.dist 164 4948 13 26 0.863158 186 2968 5 1 0.99738 0.994652 0.926554 0.998318 0.994773 0.973822 0.926554 0.999663 0.992429 0.973822 0.890413 0.998101 0.893733 0.98318 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.984127 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.35.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1169 8973 91 63 0.948864 0.98996 0.927778 0.993028 0.927778 0.985043 0.929771 0.938202 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 911 9623 23 28 0.970181 0.997616 0.975375 0.997099 0.975375 0.995182 0.970132 0.972771 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.81.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.14.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.34.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 325 41563 10 7 0.978916 0.999759 0.970149 0.999832 0.970149 0.999594 0.974318 0.974513 1 1 1 1 1 1 10 2131 0 4 26 2458 0 1 0.714286 1 0.962963 1 1 0.998126 1 1 0.999593 0.998135 1 0.844362 0.999598 0.833333 0.981107 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.124.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.75.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 4 2010 0 2 0.666667 1 1 0.999006 1 0.999008 0.816091 0.8 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.99.dist 21 2251 0 6 0.777778 1 1 0.997342 1 0.997366 0.880744 0.875 0.981132 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.71.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.110.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 52 2221 3 2 66 2274 0 6 0.962963 0.998651 0.916667 0.945455 1 0.9991 1 0.945455 0.997368 0.997805 1 0.953046 0.997442 0.954128 0.956167 0.956522 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 5 1943 0 5 0.5 1 1 0.997433 1 0.99744 0.706199 0.666667 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.113.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.68.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.74.dist 20 2256 2 0 220 3242 12 12 0.948276 0.996312 0.948276 0.996312 0.948276 0.993115 0.944588 0.948276 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 219 4382 6 49 0.817164 0.998633 0.973333 0.988942 0.973333 0.988187 0.886014 0.888438 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.53.dist 1 0.999114 0.909091 1 0.909091 0.999122 0.95304 0.952381 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.52.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 36 2241 1 0 1 0.999554 0.972973 1 0.972973 0.999561 0.986174 0.986301 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.69.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.79.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.56.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 132 4900 7 11 0.923077 0.998573 0.94964 0.99776 0.94964 0.996436 0.934437 0.93617 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.31.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 692 13527 65 81 0.895213 14 2988 0 1 0.995218 0.914135 0.933333 0.994048 1 0.914135 1 0.989836 0.999665 0.899263 1 0.904575 0.999667 0.96593 542 5859 75 79 0.872786 0.987361 0.878444 0.986696 0.878444 0.976506 0.86264 0.875606 0.965517 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.105.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.50.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 28 2600 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.97.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 80 2840 4 2 0.97561 0.998594 543 9966 29 47 0.952381 0.999296 0.920339 0.952381 0.997099 0.997949 0.949301 0.962874 0.995306 0.963855 0.949301 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.76.dist 0.99282 0.930923 0.934596 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 265 6110 49 17 0.939716 0.992044 0.843949 0.997225 0.843949 0.989753 0.88531 0.889262 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.70.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1500 35106 72 178 0.893921 0.997953 0.954198 0.994955 0.954198 0.993217 0.920069 0.923077 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.37.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 330 5650 3 12 0.964912 0.999469 0.990991 0.997881 0.990991 0.997498 0.97655 0.977778 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1147 8117 121 68 0.944033 0.985312 0.904574 0.991692 0.904574 0.980006 0.912656 0.923882 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1879 34769 124 84 0.957208 0.996446 0.938093 0.99759 0.938093 0.994356 0.944626 0.947554 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 712 18160 246 385 0.649043 0.986635 0.743215 0.97924 0.743215 0.967646 0.677679 0.692944 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 390 680902 112 124 0.758755 0.999836 0.776892 0.999818 0.776892 0.999654 0.767597 0.767717 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.58.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.28.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.20.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.43.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.54.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.46.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 7256 23638 589 1157 0.862475 0.975688 0.92492 0.953337 0.92492 0.946507 0.857976 0.892607 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 5091 60266 301 408 0.925805 0.99503 0.944177 0.993276 0.944177 0.989268 0.929106 0.9349 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.48.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 8865 69393 1083 859 0.911662 0.984633 0.891134 0.987773 0.891134 0.975786 0.887558 0.901281 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 5824 47685 573 203 0.966318 0.988126 0.910427 0.995761 0.910427 0.985705 0.930003 0.93754 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 13251 64989 1581 780 0.944409 0.976251 0.893406 0.98814 0.893406 0.970708 0.900891 0.9182 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.59.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.19.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 12602 42288 1118 945 0.930243 0.974243 0.918513 0.978142 0.918513 0.963777 0.900562 0.924341 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 3035 58432 242 419 0.878691 0.995876 0.926152 0.99288 0.926152 0.989361 0.896524 0.901798 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 8810 156536 789 618 0.934451 0.994985 0.917804 0.996068 0.917804 0.991562 0.921621 0.926052 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.25.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 10918 75363 704 586 0.949061 0.990745 0.939425 0.992284 0.939425 0.985269 0.935749 0.944219 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 12608 196366 842 3062 0.804595 0.99573 0.937398 0.984646 0.937398 0.981661 0.859031 0.865934 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.26.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 11921 135570 1904 3786 0.758961 0.98615 0.862278 0.972832 0.862278 0.962854 0.788828 0.807328 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 18933 22220 1402 1401 0.931101 0.940649 0.931055 0.940688 0.931055 0.936232 0.871746 0.931078 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.21.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.8.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 64607 1841700 6415 11019 0.854296 0.996529 0.909676 0.994053 0.909676 0.990937 0.876878 0.881117 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 61588 984617 4940 6640 0.902679 0.995008 0.925746 0.993301 0.925746 0.989053 0.908304 0.914067 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 157508 520721 10564 30607 0.837296 0.980116 0.937146 0.944485 0.937146 0.94277 0.848915 0.884412 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.11.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.23.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 239924 4325962 21668 13507 0.946703 0.995016 0.917169 0.996887 0.917169 0.992355 0.927785 0.931702 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 265717 533921 20162 69311 0.793119 0.963612 0.929474 0.885101 0.929474 0.899368 0.78512 0.8559 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 353068 4777802 34113 20827 0.944297 0.992911 0.911894 0.99566 0.911894 0.989406 0.922262 0.927813 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.27.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 716469 1577826 71379 79692 0.899905 0.956719 0.9094 0.951921 0.9094 0.938222 0.858969 0.904627 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.18.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 729638 10465151 58153 317513 0.696784 0.994474 0.926182 0.970553 0.926182 0.967532 0.787322 0.795271 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1004219 22363058 121734 181629 0.846836 0.994586 0.891884 0.991944 0.891884 0.987184 0.862364 0.868776 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.16.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.13.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1427771 2005841 63209 66294 0.955628 0.96945 0.957606 0.968007 0.957606 0.963655 0.925346 0.956616 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.17.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.10.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1349178 6988755 203141 159632 0.8942 0.971754 0.869137 0.977669 0.869137 0.958305 0.856327 0.88149 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1908374 3579731 211932 139616 0.931828 0.944106 0.900047 0.962462 0.900047 0.9398 0.869195 0.915661 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1554602 8354595 370312 288994 0.843244 0.957557 0.807622 0.966566 0.807622 0.937616 0.787382 0.825049 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 1944079 8430754 101889 96379 0.952766 0.988059 0.9502 0.988697 0.9502 0.981248 0.939861 0.951481 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.38.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 23398 117857 1537 1661 0.933716 0.987127 0.93836 0.986103 0.93836 0.977861 0.922651 0.936032 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.55.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 3831 15112 159 798 0.827609 0.989588 0.96015 0.949843 0.96015 0.95191 0.862348 0.888966 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.104.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 354 4956 18 28 0.926702 0.996381 0.951613 0.994382 0.951613 0.991412 0.934469 0.938992 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.95.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 168 2829 4 2 0.988235 0.998588 0.976744 0.999294 0.976744 0.998002 0.981416 0.982456 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.49.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 22 2172 0 17 0.564103 1 1 0.992234 1 0.992311 0.748145 0.721311 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.96.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 19 3138 0 3 0.863636 1 1 0.999045 1 0.999051 0.928876 0.926829 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.61.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 10 2135 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.91.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1764 0 6 0 1 0 0.99661 1 0.99661 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.119.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 2 1768 0 0 1 1 1 1 1 1 1 1 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.148.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0 1652 0 1 0 1 0 0.999395 1 0.999395 0 0 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.15.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.32.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.22.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 2921057 27850403 555834 1013609 0.74239 0.980433 0.840135 0.964883 0.840135 0.951472 0.762814 0.788244 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 4556730 7483608 337628 350569 0.928562 0.956832 0.931017 0.955251 0.931017 0.945933 0.885831 0.929788 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 6645121 11970756 613445 574749 0.920393 0.951253 0.915487 0.954187 0.915487 0.940003 0.870659 0.917934 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.3.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.1.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 13256478 412405482 1344084 2165709 0.859572 0.996751 0.907943 0.994776 0.907943 0.991822 0.879215 0.883096 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 14176380 242576746 2552940 1995164 0.876625 0.989585 0.847397 0.991842 0.847397 0.982594 0.852618 0.861763 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.0.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 14428491 376178981 1188980 2685464 0.843083 0.996849 0.923869 0.992912 0.923869 0.990178 0.877516 0.881629 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 20518893 170641983 2899548 4811172 0.810061 0.983292 0.876185 0.972579 0.876185 0.961228 0.820591 0.841827 Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.dist Clustering 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.4.dist tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 153057965 162470028 17147858 15474227 0.908182 0.904531 0.899252 0.913039 0.899252 0.906299 0.812502 0.903695 tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 177590171 513605490 17943277 13336140 0.93015 0.966243 0.908234 0.974691 0.908234 0.956705 0.889634 0.919062 It took 3520 seconds to cluster Merging the clustered files... It took 4 seconds to merge. /******************************************/ Running command: sens.spec(cutoff=0.03, list=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list, column=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table) NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix. It took 6239 to run sens.spec. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.sensspec /******************************************/ Done. label cutoff tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score 0.03 0.03 419088400 27646633958 45897239 43906753 0.9052 0.9983 0.9013 0.9984 0.09871 0.9968 -0.5341 0.9032 Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.sensspec mothur > remove.rare(list=current, count=current, nseqs=10, label=0.03) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list as input file for the list parameter. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.list mothur > make.shared(list=current, count=current, label=0.03) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.list as input file for the list parameter. 0.03 Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.shared mothur > classify.otu(list=current, count=current, taxonomy=current, label=0.03) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table as input file for the count parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.list as input file for the list parameter. Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v132.wang.pick.taxonomy as input file for the taxonomy parameter. 0.03 1988 Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.0.03.cons.taxonomy 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.0.03.cons.tax.summary mothur > count.groups(shared=current) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.shared as input file for the shared parameter. Mobile_Feed contains 19709. Mobile_Inlet contains 72607. Mobile_Tank contains 42168. Mobile_pooled1 contains 59900. Mobile_pooled2 contains 17157. Mobile_pooled3 contains 55838. Promega_Inlet contains 51438. Promega_feed contains 11795. Promega_pooled1 contains 69093. Promega_pooled2 contains 28188. Promega_pooled3 contains 25237. Promega_tank contains 31202. Qiagen_Blood_pooled1 contains 19371. Qiagen_Blood_pooled2 contains 7927. Qiagen_Blood_pooled3 contains 40355. Qiagen_stool_pooled1 contains 17186. Qiagen_stool_pooled2 contains 10547. Qiagen_stool_pooled3 contains 40719. fast1 contains 83507. fast10 contains 152537. fast11 contains 22259. fast12 contains 59803. fast13 contains 14854. fast14 contains 51455. fast15 contains 18050. fast16 contains 42832. fast17 contains 28580. fast18 contains 23467. fast19 contains 35513. fast2 contains 40450. fast20 contains 50204. fast21 contains 52611. fast22 contains 57833. fast23 contains 46700. fast24 contains 27083. fast3 contains 40660. fast4 contains 25341. fast5 contains 21193. fast6 contains 82. fast7 contains 48651. fast8 contains 31847. fast9 contains 53325. phenol contains 45008. slow1 contains 44280. slow10 contains 358. slow11 contains 27636. slow12 contains 16390. slow13 contains 32947. slow14 contains 20977. slow15 contains 25542. slow16 contains 62387. slow17 contains 48426. slow18 contains 40666. slow19 contains 152622. slow2 contains 20126. slow20 contains 44710. slow21 contains 60697. slow3 contains 37967. slow4 contains 14551. slow5 contains 43060. slow6 contains 30721. slow7 contains 23274. slow8 contains 6496. slow9 contains 23361. Total seqs: 2471476. Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.count.summary mothur > sub.sample(shared=current, size=6496) Using 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.shared as input file for the shared parameter. fast6 contains 82. Eliminating. slow10 contains 358. Eliminating. Sampling 6496 from each group. 0.03 Output File Names: 180802_pratima.files.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.pick.0.03.subsample.shared mothur > quit