Hi all,
I am running a test pipeline on 18S V4 MiSeq data for five samples. Any help is appreciated as I am new to Mothur.
After running chimera.vsearch I end up with larger align and count table files as expected but Mothur also creates individual align and count table files for each of my samples (e.g., stability.trim.contigs.good.unique.good.SAMPLENAME1.align and stability.trim.contigs.good.unique.good.SAMPLENAME1.count_table). When I look at the results from others, I do not see these individual files in the destination folder.
My question is: Are these individual align and count table files a normal Mothur output or does this indicate a problem in my pipeline?
Below is my logfile:
Windows version
Using Boost
mothur v.1.48.0
Last updated: 5/20/22
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://forum.mothur.org
Type 'quit()' to exit program
[NOTE]: Setting random seed to 19760620.
Interactive Mode
mothur >
make.file(inputdir=., type=fastq, prefix=stability
[ERROR]: You are missing )
[ERROR]: Invalid.
mothur >
make.file(inputdir=., type=fastq, prefix=stability)
Setting input directories to:
C:\Users\erika\Documents\MiSeqNEMtest7\
Output File Names:
C:\Users\erika\Documents\MiSeqNEMtest7\stability.files
mothur >
make.contigs(file=stability.files)
Using 4 processors.
>>>>> Processing file pair NL13_R1_MI.M06648_0253.001.FLD_ill_129_i7_IDT_i5_5.fastq - NL13_R2_MI.M06648_0253.001.FLD_ill_129_i7_IDT_i5_5.fastq (files 1 of 5) <<<<<
Making contigs...
Done.
It took 33 secs to assemble 80140 reads.
>>>>> Processing file pair NL20_R1_MI.M06648_0253.001.FLD_ill_136_i7_IDT_i5_5.fastq - NL20_R2_MI.M06648_0253.001.FLD_ill_136_i7_IDT_i5_5.fastq (files 2 of 5) <<<<<
Making contigs...
Done.
It took 30 secs to assemble 78803 reads.
>>>>> Processing file pair NL29_R1_MI.M06648_0253.001.FLD_ill_145_i7_IDT_i5_7.fastq - NL29_R2_MI.M06648_0253.001.FLD_ill_145_i7_IDT_i5_7.fastq (files 3 of 5) <<<<<
Making contigs...
Done.
It took 33 secs to assemble 85306 reads.
>>>>> Processing file pair NL37_R1_MI.M06648_0253.001.FLD_ill_153_i7_IDT_i5_8.fastq - NL37_R2_MI.M06648_0253.001.FLD_ill_153_i7_IDT_i5_8.fastq (files 4 of 5) <<<<<
Making contigs...
Done.
It took 32 secs to assemble 83243 reads.
>>>>> Processing file pair NL45_R1_MI.M06648_0253.001.FLD_ill_161_i7_IDT_i5_9.fastq - NL45_R2_MI.M06648_0253.001.FLD_ill_161_i7_IDT_i5_9.fastq (files 5 of 5) <<<<<
Making contigs...
Done.
It took 41 secs to assemble 100514 reads.
Group count:
NL13 80140
NL20 78803
NL29 85306
NL37 83243
NL45 100514
Total of all groups is 428006
It took 175 secs to process 428006 sequences.
Output File Names:
stability.trim.contigs.fasta
stability.scrap.contigs.fasta
stability.contigs_report
stability.contigs.count_table
mothur >
screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table, maxambig=0,minlength=150, maxlength=450, maxhomop=8)
Using 4 processors.
It took 5 secs to screen 428006 sequences, removed 62659.
/******************************************/
Running command: remove.seqs(accnos=stability.trim.contigs.bad.accnos.temp, count=stability.contigs.count_table)
Removed 62659 sequences from stability.contigs.count_table.
Output File Names:
stability.contigs.pick.count_table
/******************************************/
Output File Names:
stability.trim.contigs.good.fasta
stability.trim.contigs.bad.accnos
stability.contigs.good.count_table
It took 17 secs to screen 428006 sequences.
mothur >
unique.seqs(fasta= stability.trim.contigs.good.fasta, count= stability.contigs.good.count_table)
365347 97773
Output File Names:
stability.trim.contigs.good.unique.fasta
stability.trim.contigs.good.count_table
mothur >
align.seqs(fasta= stability.trim.contigs.good.unique.fasta, reference=silva.seed_v138_1.align)
Using 4 processors.
Reading in the silva.seed_v138_1.align template sequences... DONE.
It took 7 to read 7641 sequences.
Aligning sequences from stability.trim.contigs.good.unique.fasta ...
It took 340 secs to align 97773 sequences.
[WARNING]: 12 of your sequences generated alignments that eliminated too many bases, a list is provided in stability.trim.contigs.good.unique.flip.accnos.
[NOTE]: 2 of your sequences were reversed to produce a better alignment.
It took 341 seconds to align 97773 sequences.
Output File Names:
stability.trim.contigs.good.unique.align
stability.trim.contigs.good.unique.align_report
stability.trim.contigs.good.unique.flip.accnos
mothur >
screen.seqs(fasta= stability.trim.contigs.good.unique.align, count= stability.trim.contigs.good.count_table, start=33287, end=41796)
Using 4 processors.
It took 49 secs to screen 97773 sequences, removed 4750.
/******************************************/
Running command: remove.seqs(accnos=stability.trim.contigs.good.unique.bad.accnos.temp, count=stability.trim.contigs.good.count_table)
Removed 8097 sequences from stability.trim.contigs.good.count_table.
Output File Names:
stability.trim.contigs.good.pick.count_table
/******************************************/
Output File Names:
stability.trim.contigs.good.unique.good.align
stability.trim.contigs.good.unique.bad.accnos
stability.trim.contigs.good.good.count_table
It took 96 secs to screen 97773 sequences.
mothur >
filter.seqs(fasta=current, vertical=T, trump=.)
Using stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 4 processors.
Creating Filter...
It took 41 secs to create filter for 93023 sequences.
Running Filter...
It took 37 secs to filter 93023 sequences.
Length of filtered alignment: 802
Number of columns removed: 49198
Length of the original alignment: 50000
Number of sequences used to construct filter: 93023
Output File Names:
stability.filter
stability.trim.contigs.good.unique.good.filter.fasta
mothur >
unique.seqs(fasta=current, count=current)
Using stability.trim.contigs.good.good.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.fasta as input file for the fasta parameter.
93023 92937
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.fasta
stability.trim.contigs.good.unique.good.filter.count_table
mothur >
pre.cluster(fasta=current, count=current, diffs=2)
Using stability.trim.contigs.good.unique.good.filter.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.fasta as input file for the fasta parameter.
Using 4 processors.
/******************************************/
Splitting by sample:
Using 4 processors.
Selecting sequences for groups NL29
Selecting sequences for groups NL13
Selecting sequences for groups NL20
Selecting sequences for groups NL37-NL45
Selected 17628 sequences from NL20.
Selected 22638 sequences from NL13.
Selected 19577 sequences from NL29.
Selected 20876 sequences from NL37.
Selected 17791 sequences from NL45.
It took 7 seconds to split the dataset by sample.
/******************************************/
Processing group NL20:
Processing group NL29:
Processing group NL13:
Processing group NL37:
NL20 17628 5881 11747
Total number of sequences before pre.cluster was 17628.
pre.cluster removed 11747 sequences.
It took 8 secs to cluster 17628 sequences.
NL29 19577 6474 13103
Total number of sequences before pre.cluster was 19577.
pre.cluster removed 13103 sequences.
It took 8 secs to cluster 19577 sequences.
NL37 20876 6976 13900
Total number of sequences before pre.cluster was 20876.
pre.cluster removed 13900 sequences.
It took 10 secs to cluster 20876 sequences.
Processing group NL45:
NL13 22638 8200 14438
Total number of sequences before pre.cluster was 22638.
pre.cluster removed 14438 sequences.
It took 11 secs to cluster 22638 sequences.
NL45 17791 5589 12202
Total number of sequences before pre.cluster was 17791.
pre.cluster removed 12202 sequences.
It took 4 secs to cluster 17791 sequences.
Deconvoluting count table results...
It took 0 secs to merge 33120 sequences group data.
/******************************************/
Running get.seqs:
Selected 32899 sequences from stability.trim.contigs.good.unique.good.filter.unique.fasta.
/******************************************/
It took 25 secs to run pre.cluster.
Using 4 processors.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta
stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table
stability.trim.contigs.good.unique.good.filter.unique.precluster.NL13.map
stability.trim.contigs.good.unique.good.filter.unique.precluster.NL20.map
stability.trim.contigs.good.unique.good.filter.unique.precluster.NL29.map
stability.trim.contigs.good.unique.good.filter.unique.precluster.NL37.map
stability.trim.contigs.good.unique.good.filter.unique.precluster.NL45.map
mothur >
chimera.vsearch(fasta=current, count=current, dereplicate=t)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using 4 processors.
Checking sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta ...
/******************************************/
Splitting by sample:
Using 4 processors.
Selecting sequences for groups NL29
Selecting sequences for groups NL13
Selecting sequences for groups NL20
Selecting sequences for groups NL37-NL45
Selected 6474 sequences from NL29.
Selected 5881 sequences from NL20.
Selected 8200 sequences from NL13.
Selected 6976 sequences from NL37.
Selected 5589 sequences from NL45.
It took 3 seconds to split the dataset by sample.
/******************************************/
It took 26 secs to check 5881 sequences from group NL20.
It took 28 secs to check 6474 sequences from group NL29.
It took 30 secs to check 6976 sequences from group NL37.
It took 34 secs to check 8200 sequences from group NL13.
It took 15 secs to check 5589 sequences from group NL45.
It took 45 secs to check 33120 sequences.
Removing chimeras from your input files:
/******************************************/
Running command: remove.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos)
Removed 2952 sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta
/******************************************/
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta
mothur >
classify.seqs(fasta=current, count=current, reference=silva.nr_v138_1.align, taxonomy=silva.nr_v138_1.tax)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta as input file for the fasta parameter.
Using 4 processors.
Generating search database... DONE.
It took 272 seconds generate search database.
Reading in the silva.nr_v138_1.tax taxonomy... DONE.
Calculating template taxonomy tree... DONE.
Calculating template probabilities... DONE.
It took 519 seconds get probabilities.
Classifying sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta ...
It took 836 secs to classify 29947 sequences.
It took 6 secs to create the summary file for 29947 sequences.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.taxonomy
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.tax.summary
mothur >
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Vertebrata-Fungi)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta as input file for the fasta parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.taxonomy as input file for the taxonomy parameter.
/******************************************/
Running command: remove.seqs(accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.accnos, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta)
Removed 728 sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta.
Removed 18357 sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.fasta
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table
/******************************************/
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.taxonomy
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.accnos
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.fasta
mothur >
summary.tax(taxonomy=current, count=current)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.taxonomy as input file for the taxonomy parameter.
It took 1 secs to create the summary file for 329009 sequences.
Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.tax.summary
mothur >
rename.file(fasta=current, count=current, taxonomy=current, prefix=final)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.fasta as input file for the fasta parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.taxonomy as input file for the taxonomy parameter.
Current files saved by mothur:
accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.nr_v138_1.wang.accnos
fasta=final.fasta
taxonomy=final.taxonomy
contigsreport=stability.contigs_report
count=final.count_table
processors=4
file=C:\Users\erika\Documents\MiSeqNEMtest7\stability.files
mothur >
: cluster.split(fasta=current, count=current, taxonomy=current, taxlevel=4, cutoff=0.03)
[ERROR]: Invalid command.
[ERROR]: did not complete : cluster.split.
mothur >
: cluster.split(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy, taxlevel=4, cutoff=0.03)
[ERROR]: Invalid command.
[ERROR]: did not complete : cluster.split.
mothur >
cluster.split(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy, taxlevel=4, cutoff=0.03)
Using 4 processors.
Splitting the file...
/******************************************/
Selecting sequences for group Tylenchida (1 of 16)
Number of unique sequences: 7903
Selected 65564 sequences from final.count_table.
Calculating distances for group Tylenchida (1 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 63 secs to find distances for 7903 sequences. 1209651 distances below cutoff 0.03.
Output File Names:
final.0.dist
/******************************************/
/******************************************/
Selecting sequences for group Chromadorea_unclassified (2 of 16)
Number of unique sequences: 11814
Selected 166367 sequences from final.count_table.
Calculating distances for group Chromadorea_unclassified (2 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 141 secs to find distances for 11814 sequences. 8484186 distances below cutoff 0.03.
Output File Names:
final.1.dist
/******************************************/
/******************************************/
Selecting sequences for group Triplonchida (3 of 16)
Number of unique sequences: 111
Selected 1252 sequences from final.count_table.
Calculating distances for group Triplonchida (3 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 111 sequences. 1475 distances below cutoff 0.03.
Output File Names:
final.2.dist
/******************************************/
/******************************************/
Selecting sequences for group Eukaryota_unclassified (4 of 16)
Number of unique sequences: 3749
Selected 42361 sequences from final.count_table.
Calculating distances for group Eukaryota_unclassified (4 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 12 secs to find distances for 3749 sequences. 525073 distances below cutoff 0.03.
Output File Names:
final.3.dist
/******************************************/
/******************************************/
Selecting sequences for group Rhabditida (5 of 16)
Number of unique sequences: 2888
Selected 35853 sequences from final.count_table.
Calculating distances for group Rhabditida (5 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 9 secs to find distances for 2888 sequences. 1170484 distances below cutoff 0.03.
Output File Names:
final.4.dist
/******************************************/
/******************************************/
Selecting sequences for group Diplogasterida (6 of 16)
Number of unique sequences: 875
Selected 8633 sequences from final.count_table.
Calculating distances for group Diplogasterida (6 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 1 secs to find distances for 875 sequences. 105271 distances below cutoff 0.03.
Output File Names:
final.5.dist
/******************************************/
/******************************************/
Selecting sequences for group Dorylaimia_or (7 of 16)
Number of unique sequences: 414
Selected 3500 sequences from final.count_table.
Calculating distances for group Dorylaimia_or (7 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 414 sequences. 23454 distances below cutoff 0.03.
Output File Names:
final.6.dist
/******************************************/
/******************************************/
Selecting sequences for group Nematozoa_unclassified (8 of 16)
Number of unique sequences: 829
Selected 1176 sequences from final.count_table.
Calculating distances for group Nematozoa_unclassified (8 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 1 secs to find distances for 829 sequences. 250341 distances below cutoff 0.03.
Output File Names:
final.7.dist
/******************************************/
/******************************************/
Selecting sequences for group Haplotaxida (9 of 16)
Number of unique sequences: 25
Selected 344 sequences from final.count_table.
Calculating distances for group Haplotaxida (9 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 25 sequences. 184 distances below cutoff 0.03.
Output File Names:
final.8.dist
/******************************************/
/******************************************/
Selecting sequences for group Araeolaimida (10 of 16)
Number of unique sequences: 484
Selected 3670 sequences from final.count_table.
Calculating distances for group Araeolaimida (10 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 1 secs to find distances for 484 sequences. 25078 distances below cutoff 0.03.
Output File Names:
final.9.dist
/******************************************/
/******************************************/
Selecting sequences for group Enoplea_unclassified (11 of 16)
Number of unique sequences: 80
Selected 188 sequences from final.count_table.
Calculating distances for group Enoplea_unclassified (11 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 80 sequences. 1970 distances below cutoff 0.03.
Output File Names:
final.10.dist
/******************************************/
/******************************************/
Selecting sequences for group Adinetida (12 of 16)
Number of unique sequences: 23
Selected 59 sequences from final.count_table.
Calculating distances for group Adinetida (12 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 23 sequences. 78 distances below cutoff 0.03.
Output File Names:
final.11.dist
/******************************************/
/******************************************/
Selecting sequences for group Parachaela (13 of 16)
Number of unique sequences: 5
Selected 19 sequences from final.count_table.
Calculating distances for group Parachaela (13 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 5 sequences. 3 distances below cutoff 0.03.
Output File Names:
final.12.dist
/******************************************/
/******************************************/
Selecting sequences for group Clitellata_unclassified (14 of 16)
Number of unique sequences: 11
Selected 13 sequences from final.count_table.
Calculating distances for group Clitellata_unclassified (14 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 11 sequences. 45 distances below cutoff 0.03.
Output File Names:
final.13.dist
/******************************************/
/******************************************/
Selecting sequences for group Animalia_or (15 of 16)
Number of unique sequences: 2
Selected 2 sequences from final.count_table.
Calculating distances for group Animalia_or (15 of 16):
Sequence Time Num_Dists_Below_Cutoff
It took 0 secs to find distances for 2 sequences. 0 distances below cutoff 0.03.
Output File Names:
final.14.dist
/******************************************/
/******************************************/
Selecting sequences for group Liliopsida (16 of 16)
Number of unique sequences: 2
Selected 2 sequences from final.count_table.
Calculating distances for group Liliopsida (16 of 16):
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:
final.15.dist
/******************************************/
/******************************************/
Finding singletons (ignore 'Removing group' messages):
Running command: remove.seqs()
Removed 329001 sequences from final.count_table.
/******************************************/
It took 232 seconds to split the distance file.
final.0.disttemp
final.5.disttemp
final.2.disttemp
final.12.disttemp
Clustering final.12.disttemp
Clustering final.13.disttemp
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 7 0 3 0 10 0 45 0 0 1 1
Clustering final.15.disttemp
0 0 0.181818 0.7 1 1 0.181818 0 0 0.7
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
0 0 0 0 1 0 0
0 0 0 1 0 0 0
Clustering final.8.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
184 108 8 0 1 0.931034 0.958333 1 0.958333 0.973333 0.944585 0.978723
Clustering final.2.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
1445 4602 28 30 0.979661 0.993952 0.980991 0.993523 0.980991 0.9905 0.974064 0.980326
Clustering final.10.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
1959 1185 5 11 0.994416 0.995798 0.997454 0.990803 0.997454 0.994937 0.989235 0.995933
Clustering final.9.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
21892 90163 1645 3186 0.872956 0.982082 0.93011 0.96587 0.93011 0.958669 0.87527 0.900627
Clustering final.5.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
102969 275200 1904 2302 0.978133 0.993129 0.981845 0.991705 0.981845 0.989 0.972405 0.979985
Clustering final.7.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
250016 89308 3557 325 0.998702 0.961697 0.985972 0.996374 0.985972 0.988689 0.971311 0.992296
Clustering final.3.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
519952 6.48142e+06 19133 5121 0.990247 0.997057 0.964508 0.999211 0.964508 0.996548 0.97544 0.977208
Clustering final.6.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
23147 61245 792 307 0.986911 0.987233 0.966916 0.995012 0.966916 0.987145 0.968017 0.976811
Clustering final.11.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
73 175 0 5 0.935897 1 1 0.972222 1 0.980237 0.953887 0.966887
Clustering final.4.disttemp
Clustering final.0.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
1.16217e+06 2.96566e+06 32682 8313 0.992898 0.9891 0.972648 0.997205 0.972648 0.990166 0.975906 0.982668
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
1.18525e+06 2.99823e+07 32841 24401 0.979828 0.998906 0.973039 0.999187 0.973039 0.998167 0.975474 0.976422
Clustering final.1.disttemp
tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
7.83585e+06 6.10008e+07 294450 648334 0.923583 0.995196 0.963784 0.989483 0.963784 0.986489 0.935864 0.943255
It took 159 seconds to cluster
Merging the clustered files...
It took 0 seconds to merge.
/******************************************/
Running command: sens.spec(cutoff=0.03, list=final.opti_mcc.list, column=final.dist, count=final.count_table)
NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.
label cutoff numotus tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
0.03
0.03 0.03 2553 1.11049e+07 4.14676e+08 387045 692384 0.94131 0.999068 0.96632 0.998333 0.96632 0.997471 0.952438 0.953651
It took 162 to run sens.spec.
Output File Names:
final.opti_mcc.sensspec
/******************************************/
Done.
label cutoff numotus tp tn fp fn sensitivity specificity ppv npv fdr accuracy mcc f1score
0.03 0.03 2553 1.11049e+07 4.14676e+08 387045 692384 0.9413 0.9991 0.9663 0.9983 0.9663 0.9975 0.9524 0.9537
Output File Names:
final.dist
final.opti_mcc.list
final.opti_mcc.sensspec
mothur >
make.shared(list=final.opti_mcc.list, count=final.count_table, label=0.03)
0.03
Output File Names:
final.opti_mcc.shared
mothur >
classify.otu(list=final.opti_mcc.list, count=final.count_table, taxonomy=final.taxonomy, label=0.03)
0.03
Output File Names:
final.opti_mcc.0.03.cons.taxonomy
final.opti_mcc.0.03.cons.tax.summary
mothur >
count.groups(shared=final.opti_mcc.shared)
NL13 contains 64554.
NL20 contains 44657.
NL29 contains 69452.
NL37 contains 68144.
NL45 contains 82202.
Size of smallest group: 44657.
Total seqs: 329009.
Output File Names:
final.opti_mcc.count.summary
mothur >
sub.sample(shared=final.opti_mcc.shared)
0.03
Sampling 44657 from each group.
Output File Names:
final.opti_mcc.0.03.subsample.shared
mothur >
rarefaction.single(shared=final.opti_mcc.shared, calc=sobs, freq=100)
Using 4 processors.
Processing group NL13
0.03
Processing group NL20
0.03
Processing group NL29
0.03
Processing group NL37
0.03
Processing group NL45
0.03
It took 28 secs to run rarefaction.single.
Output File Names:
final.opti_mcc.groups.rarefaction
mothur >