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kitome.logfile
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Linux version
Using ReadLine
Using default file location /share/apps/mothur/1.39.0/intel/2017_update-1/bin/
Running 64Bit Version
mothur v.1.39.0
Last updated: 1/23/2017
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
Script Mode
mothur > make.contigs(file=stability.files)
Using 1 processors.
>>>>> Processing file pair 120_D1_MB_S218_L001_R1_001.fastq - 120_D1_MB_S218_L001_R2_001.fastq (files 1 of 70) <<<<<
Making contigs...
Done.
It took 78 secs to assemble 82505 reads.
>>>>> Processing file pair 120_D1_QIA_S191_L001_R1_001.fastq - 120_D1_QIA_S191_L001_R2_001.fastq (files 2 of 70) <<<<<
Making contigs...
Done.
It took 34 secs to assemble 36284 reads.
>>>>> Processing file pair 120_D2_MB_S214_L001_R1_001.fastq - 120_D2_MB_S214_L001_R2_001.fastq (files 3 of 70) <<<<<
Making contigs...
Done.
It took 48 secs to assemble 51127 reads.
>>>>> Processing file pair 120_D2_QIA_S220_L001_R1_001.fastq - 120_D2_QIA_S220_L001_R2_001.fastq (files 4 of 70) <<<<<
Making contigs...
Done.
It took 39 secs to assemble 42090 reads.
>>>>> Processing file pair 120_D3_MB_S208_L001_R1_001.fastq - 120_D3_MB_S208_L001_R2_001.fastq (files 5 of 70) <<<<<
Making contigs...
Done.
It took 53 secs to assemble 57325 reads.
>>>>> Processing file pair 120_D3_QIA_S184_L001_R1_001.fastq - 120_D3_QIA_S184_L001_R2_001.fastq (files 6 of 70) <<<<<
Making contigs...
Done.
It took 2 secs to assemble 1760 reads.
>>>>> Processing file pair 120_D4_MB_S182_L001_R1_001.fastq - 120_D4_MB_S182_L001_R2_001.fastq (files 7 of 70) <<<<<
Making contigs...
Done.
It took 28 secs to assemble 29976 reads.
>>>>> Processing file pair 120_D4_QIA_S221_L001_R1_001.fastq - 120_D4_QIA_S221_L001_R2_001.fastq (files 8 of 70) <<<<<
Making contigs...
Done.
It took 2 secs to assemble 2251 reads.
>>>>> Processing file pair 120_D5_MB_S172_L001_R1_001.fastq - 120_D5_MB_S172_L001_R2_001.fastq (files 9 of 70) <<<<<
Making contigs...
Done.
It took 18 secs to assemble 19404 reads.
>>>>> Processing file pair 120_D5_QIA_S143_L001_R1_001.fastq - 120_D5_QIA_S143_L001_R2_001.fastq (files 10 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 165 reads.
>>>>> Processing file pair 120_SD_MB_S187_L001_R1_001.fastq - 120_SD_MB_S187_L001_R2_001.fastq (files 11 of 70) <<<<<
Making contigs...
Done.
It took 33 secs to assemble 35306 reads.
>>>>> Processing file pair 120_SD_QIA_S157_L001_R1_001.fastq - 120_SD_QIA_S157_L001_R2_001.fastq (files 12 of 70) <<<<<
Making contigs...
Done.
It took 49 secs to assemble 52141 reads.
>>>>> Processing file pair 226_D1_MB_S209_L001_R1_001.fastq - 226_D1_MB_S209_L001_R2_001.fastq (files 13 of 70) <<<<<
Making contigs...
Done.
It took 46 secs to assemble 49332 reads.
>>>>> Processing file pair 226_D1_QIA_S213_L001_R1_001.fastq - 226_D1_QIA_S213_L001_R2_001.fastq (files 14 of 70) <<<<<
Making contigs...
Done.
It took 48 secs to assemble 51223 reads.
>>>>> Processing file pair 226_D2_MB_S145_L001_R1_001.fastq - 226_D2_MB_S145_L001_R2_001.fastq (files 15 of 70) <<<<<
Making contigs...
Done.
It took 37 secs to assemble 39955 reads.
>>>>> Processing file pair 226_D2_QIA_S201_L001_R1_001.fastq - 226_D2_QIA_S201_L001_R2_001.fastq (files 16 of 70) <<<<<
Making contigs...
Done.
It took 40 secs to assemble 43122 reads.
>>>>> Processing file pair 226_D3_MB_S161_L001_R1_001.fastq - 226_D3_MB_S161_L001_R2_001.fastq (files 17 of 70) <<<<<
Making contigs...
Done.
It took 1 secs to assemble 619 reads.
>>>>> Processing file pair 226_D3_QIA_S169_L001_R1_001.fastq - 226_D3_QIA_S169_L001_R2_001.fastq (files 18 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 130 reads.
>>>>> Processing file pair 226_D4_MB_S164_L001_R1_001.fastq - 226_D4_MB_S164_L001_R2_001.fastq (files 19 of 70) <<<<<
Making contigs...
Done.
It took 1 secs to assemble 970 reads.
>>>>> Processing file pair 226_D4_QIA_S204_L001_R1_001.fastq - 226_D4_QIA_S204_L001_R2_001.fastq (files 20 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 307 reads.
>>>>> Processing file pair 226_D5_MB_S181_L001_R1_001.fastq - 226_D5_MB_S181_L001_R2_001.fastq (files 21 of 70) <<<<<
Making contigs...
Done.
It took 33 secs to assemble 34697 reads.
>>>>> Processing file pair 226_D5_QIA_S176_L001_R1_001.fastq - 226_D5_QIA_S176_L001_R2_001.fastq (files 22 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 88 reads.
>>>>> Processing file pair 226_SD_MB_S186_L001_R1_001.fastq - 226_SD_MB_S186_L001_R2_001.fastq (files 23 of 70) <<<<<
Making contigs...
Done.
It took 39 secs to assemble 42534 reads.
>>>>> Processing file pair 226_SD_QIA_S185_L001_R1_001.fastq - 226_SD_QIA_S185_L001_R2_001.fastq (files 24 of 70) <<<<<
Making contigs...
Done.
It took 50 secs to assemble 53877 reads.
>>>>> Processing file pair 294_D1_MB_S197_L001_R1_001.fastq - 294_D1_MB_S197_L001_R2_001.fastq (files 25 of 70) <<<<<
Making contigs...
Done.
It took 51 secs to assemble 54707 reads.
>>>>> Processing file pair 294_D1_QIA_S212_L001_R1_001.fastq - 294_D1_QIA_S212_L001_R2_001.fastq (files 26 of 70) <<<<<
Making contigs...
Done.
It took 35 secs to assemble 37141 reads.
>>>>> Processing file pair 294_D2_MB_S142_L001_R1_001.fastq - 294_D2_MB_S142_L001_R2_001.fastq (files 27 of 70) <<<<<
Making contigs...
Done.
It took 39 secs to assemble 41596 reads.
>>>>> Processing file pair 294_D2_QIA_S179_L001_R1_001.fastq - 294_D2_QIA_S179_L001_R2_001.fastq (files 28 of 70) <<<<<
Making contigs...
Done.
It took 28 secs to assemble 29964 reads.
>>>>> Processing file pair 294_D3_MB_S155_L001_R1_001.fastq - 294_D3_MB_S155_L001_R2_001.fastq (files 29 of 70) <<<<<
Making contigs...
Done.
It took 59 secs to assemble 63219 reads.
>>>>> Processing file pair 294_D3_QIA_S200_L001_R1_001.fastq - 294_D3_QIA_S200_L001_R2_001.fastq (files 30 of 70) <<<<<
Making contigs...
Done.
It took 5 secs to assemble 5820 reads.
>>>>> Processing file pair 294_D4_MB_S199_L001_R1_001.fastq - 294_D4_MB_S199_L001_R2_001.fastq (files 31 of 70) <<<<<
Making contigs...
Done.
It took 60 secs to assemble 64400 reads.
>>>>> Processing file pair 294_D4_QIA_S195_L001_R1_001.fastq - 294_D4_QIA_S195_L001_R2_001.fastq (files 32 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 228 reads.
>>>>> Processing file pair 294_D5_MB_S141_L001_R1_001.fastq - 294_D5_MB_S141_L001_R2_001.fastq (files 33 of 70) <<<<<
Making contigs...
Done.
It took 27 secs to assemble 28799 reads.
>>>>> Processing file pair 294_D5_QIA_S205_L001_R1_001.fastq - 294_D5_QIA_S205_L001_R2_001.fastq (files 34 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 227 reads.
>>>>> Processing file pair 294_SD_MB_S167_L001_R1_001.fastq - 294_SD_MB_S167_L001_R2_001.fastq (files 35 of 70) <<<<<
Making contigs...
Done.
It took 16 secs to assemble 16604 reads.
>>>>> Processing file pair 294_SD_QIA_S154_L001_R1_001.fastq - 294_SD_QIA_S154_L001_R2_001.fastq (files 36 of 70) <<<<<
Making contigs...
Done.
It took 55 secs to assemble 59146 reads.
>>>>> Processing file pair 390_D1_MB_S210_L001_R1_001.fastq - 390_D1_MB_S210_L001_R2_001.fastq (files 37 of 70) <<<<<
Making contigs...
Done.
It took 56 secs to assemble 60366 reads.
>>>>> Processing file pair 390_D1_QIA_S170_L001_R1_001.fastq - 390_D1_QIA_S170_L001_R2_001.fastq (files 38 of 70) <<<<<
Making contigs...
Done.
It took 17 secs to assemble 18238 reads.
>>>>> Processing file pair 390_D2_MB_S162_L001_R1_001.fastq - 390_D2_MB_S162_L001_R2_001.fastq (files 39 of 70) <<<<<
Making contigs...
Done.
It took 17 secs to assemble 18232 reads.
>>>>> Processing file pair 390_D2_QIA_S160_L001_R1_001.fastq - 390_D2_QIA_S160_L001_R2_001.fastq (files 40 of 70) <<<<<
Making contigs...
Done.
It took 80 secs to assemble 86061 reads.
>>>>> Processing file pair 390_D3_MB_S224_L001_R1_001.fastq - 390_D3_MB_S224_L001_R2_001.fastq (files 41 of 70) <<<<<
Making contigs...
Done.
It took 49 secs to assemble 52388 reads.
>>>>> Processing file pair 390_D3_QIA_S153_L001_R1_001.fastq - 390_D3_QIA_S153_L001_R2_001.fastq (files 42 of 70) <<<<<
Making contigs...
Done.
It took 33 secs to assemble 35181 reads.
>>>>> Processing file pair 390_D4_MB_S222_L001_R1_001.fastq - 390_D4_MB_S222_L001_R2_001.fastq (files 43 of 70) <<<<<
Making contigs...
Done.
It took 13 secs to assemble 13885 reads.
>>>>> Processing file pair 390_D4_QIA_S193_L001_R1_001.fastq - 390_D4_QIA_S193_L001_R2_001.fastq (files 44 of 70) <<<<<
Making contigs...
Done.
It took 4 secs to assemble 4144 reads.
>>>>> Processing file pair 390_D5_MB_S192_L001_R1_001.fastq - 390_D5_MB_S192_L001_R2_001.fastq (files 45 of 70) <<<<<
Making contigs...
Done.
It took 34 secs to assemble 37322 reads.
>>>>> Processing file pair 390_D5_QIA_S178_L001_R1_001.fastq - 390_D5_QIA_S178_L001_R2_001.fastq (files 46 of 70) <<<<<
Making contigs...
Done.
It took 1 secs to assemble 873 reads.
>>>>> Processing file pair 390_SD_MB_S194_L001_R1_001.fastq - 390_SD_MB_S194_L001_R2_001.fastq (files 47 of 70) <<<<<
Making contigs...
Done.
It took 28 secs to assemble 29511 reads.
>>>>> Processing file pair 390_SD_QIA_S147_L001_R1_001.fastq - 390_SD_QIA_S147_L001_R2_001.fastq (files 48 of 70) <<<<<
Making contigs...
Done.
It took 48 secs to assemble 51833 reads.
>>>>> Processing file pair 52_D1_MB_S156_L001_R1_001.fastq - 52_D1_MB_S156_L001_R2_001.fastq (files 49 of 70) <<<<<
Making contigs...
Done.
It took 39 secs to assemble 42364 reads.
>>>>> Processing file pair 52_D1_QIA_S151_L001_R1_001.fastq - 52_D1_QIA_S151_L001_R2_001.fastq (files 50 of 70) <<<<<
Making contigs...
Done.
It took 61 secs to assemble 65385 reads.
>>>>> Processing file pair 52_D2_MB_S148_L001_R1_001.fastq - 52_D2_MB_S148_L001_R2_001.fastq (files 51 of 70) <<<<<
Making contigs...
Done.
It took 52 secs to assemble 55649 reads.
>>>>> Processing file pair 52_D2_QIA_S188_L001_R1_001.fastq - 52_D2_QIA_S188_L001_R2_001.fastq (files 52 of 70) <<<<<
Making contigs...
Done.
It took 30 secs to assemble 30819 reads.
>>>>> Processing file pair 52_D3_MB_S183_L001_R1_001.fastq - 52_D3_MB_S183_L001_R2_001.fastq (files 53 of 70) <<<<<
Making contigs...
Done.
It took 11 secs to assemble 11746 reads.
>>>>> Processing file pair 52_D3_QIA_S211_L001_R1_001.fastq - 52_D3_QIA_S211_L001_R2_001.fastq (files 54 of 70) <<<<<
Making contigs...
Done.
It took 11 secs to assemble 12023 reads.
>>>>> Processing file pair 52_D4_MB_S190_L001_R1_001.fastq - 52_D4_MB_S190_L001_R2_001.fastq (files 55 of 70) <<<<<
Making contigs...
Done.
It took 30 secs to assemble 31908 reads.
>>>>> Processing file pair 52_D4_QIA_S219_L001_R1_001.fastq - 52_D4_QIA_S219_L001_R2_001.fastq (files 56 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 364 reads.
>>>>> Processing file pair 52_D5_MB_S149_L001_R1_001.fastq - 52_D5_MB_S149_L001_R2_001.fastq (files 57 of 70) <<<<<
Making contigs...
Done.
It took 32 secs to assemble 34051 reads.
>>>>> Processing file pair 52_D5_QIA_S166_L001_R1_001.fastq - 52_D5_QIA_S166_L001_R2_001.fastq (files 58 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 97 reads.
>>>>> Processing file pair 52_SD_MB_S207_L001_R1_001.fastq - 52_SD_MB_S207_L001_R2_001.fastq (files 59 of 70) <<<<<
Making contigs...
Done.
It took 68 secs to assemble 72522 reads.
>>>>> Processing file pair 52_SD_QIA_S202_L001_R1_001.fastq - 52_SD_QIA_S202_L001_R2_001.fastq (files 60 of 70) <<<<<
Making contigs...
Done.
It took 46 secs to assemble 49478 reads.
>>>>> Processing file pair BufferAE_S225_L001_R1_001.fastq - BufferAE_S225_L001_R2_001.fastq (files 61 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 117 reads.
>>>>> Processing file pair BufferC6_S163_L001_R1_001.fastq - BufferC6_S163_L001_R2_001.fastq (files 62 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 128 reads.
>>>>> Processing file pair controlkit_Qia_PBS_S158_L001_R1_001.fastq - controlkit_Qia_PBS_S158_L001_R2_001.fastq (files 63 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 160 reads.
>>>>> Processing file pair controlkitMB_S206_L001_R1_001.fastq - controlkitMB_S206_L001_R2_001.fastq (files 64 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 95 reads.
>>>>> Processing file pair controlkitMBPBS_S171_L001_R1_001.fastq - controlkitMBPBS_S171_L001_R2_001.fastq (files 65 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 67 reads.
>>>>> Processing file pair EMPTY_A1_S139_L001_R1_001.fastq - EMPTY_A1_S139_L001_R2_001.fastq (files 66 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 103 reads.
>>>>> Processing file pair EMPTY_B1_S150_L001_R1_001.fastq - EMPTY_B1_S150_L001_R2_001.fastq (files 67 of 70) <<<<<
Making contigs...
Done.
It took 1 secs to assemble 111 reads.
>>>>> Processing file pair mockB07292016_S215_L001_R1_001.fastq - mockB07292016_S215_L001_R2_001.fastq (files 68 of 70) <<<<<
Making contigs...
Done.
It took 59 secs to assemble 64465 reads.
>>>>> Processing file pair PBS_S198_L001_R1_001.fastq - PBS_S198_L001_R2_001.fastq (files 69 of 70) <<<<<
Making contigs...
Done.
It took 1 secs to assemble 80 reads.
>>>>> Processing file pair waterB07292016_S226_L001_R1_001.fastq - waterB07292016_S226_L001_R2_001.fastq (files 70 of 70) <<<<<
Making contigs...
Done.
It took 0 secs to assemble 145 reads.
It took 1876 secs to process 2008950 sequences.
Group count:
120_D1_MB 82505
120_D1_QIA 36284
120_D2_MB 51127
120_D2_QIA 42090
120_D3_MB 57325
120_D3_QIA 1760
120_D4_MB 29976
120_D4_QIA 2251
120_D5_MB 19404
120_D5_QIA 165
120_SD_MB 35306
120_SD_QIA 52141
226_D1_MB 49332
226_D1_QIA 51223
226_D2_MB 39955
226_D2_QIA 43122
226_D3_MB 619
226_D3_QIA 130
226_D4_MB 970
226_D4_QIA 307
226_D5_MB 34697
226_D5_QIA 88
226_SD_MB 42534
226_SD_QIA 53877
294_D1_MB 54707
294_D1_QIA 37141
294_D2_MB 41596
294_D2_QIA 29964
294_D3_MB 63219
294_D3_QIA 5820
294_D4_MB 64400
294_D4_QIA 228
294_D5_MB 28799
294_D5_QIA 227
294_SD_MB 16604
294_SD_QIA 59146
390_D1_MB 60366
390_D1_QIA 18238
390_D2_MB 18232
390_D2_QIA 86061
390_D3_MB 52388
390_D3_QIA 35181
390_D4_MB 13885
390_D4_QIA 4144
390_D5_MB 37322
390_D5_QIA 873
390_SD_MB 29511
390_SD_QIA 51833
52_D1_MB 42364
52_D1_QIA 65385
52_D2_MB 55649
52_D2_QIA 30819
52_D3_MB 11746
52_D3_QIA 12023
52_D4_MB 31908
52_D4_QIA 364
52_D5_MB 34051
52_D5_QIA 97
52_SD_MB 72522
52_SD_QIA 49478
BufferAE 117
BufferC6 128
EMPTY_A1 103
EMPTY_B1 111
PBS 80
controlkitMB 95
controlkitMBPBS 67
controlkit_Qia_PBS 160
mockB07292016 64465
waterB07292016 145
Total of all groups is 2008950
Output File Names:
stability.trim.contigs.fasta
stability.trim.contigs.qual
stability.contigs.report
stability.scrap.contigs.fasta
stability.scrap.contigs.qual
stability.contigs.groups
[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.
mothur > summary.seqs(fasta=stability.trim.contigs.fasta)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 81 81 0 3 1
2.5%-tile: 1 252 252 0 4 50224
25%-tile: 1 253 253 0 4 502238
Median: 1 253 253 0 5 1004476
75%-tile: 1 253 253 0 5 1506713
97.5%-tile: 1 253 253 7 6 1958727
Maximum: 1 502 502 306 250 2008950
Mean: 1 253.069 253.069 0.715999 4.7577
# of Seqs: 2008950
Output File Names:
stability.trim.contigs.summary
It took 24 secs to summarize 2008950 sequences.
mothur > screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, summary=stability.trim.contigs.summary, maxambig=0, maxlength=275)
Using 1 processors.
Output File Names:
stability.trim.contigs.good.summary
stability.trim.contigs.good.fasta
stability.trim.contigs.bad.accnos
stability.contigs.good.groups
It took 29 secs to screen 2008950 sequences.
mothur > unique.seqs(fasta=stability.trim.contigs.good.fasta)
1704820 127429
Output File Names:
stability.trim.contigs.good.names
stability.trim.contigs.good.unique.fasta
mothur > count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
Using 1 processors.
It took 10 secs to create a table for 1704820 sequences.
Total number of sequences: 1704820
Output File Names:
stability.trim.contigs.good.count_table
mothur > summary.seqs(count=stability.trim.contigs.good.count_table)
Using stability.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 250 250 0 3 1
2.5%-tile: 1 252 252 0 4 42621
25%-tile: 1 253 253 0 4 426206
Median: 1 253 253 0 5 852411
75%-tile: 1 253 253 0 5 1278616
97.5%-tile: 1 253 253 0 6 1662200
Maximum: 1 273 273 0 10 1704820
Mean: 1 252.891 252.891 0 4.65258
# of unique seqs: 127429
total # of seqs: 1704820
Output File Names:
stability.trim.contigs.good.unique.summary
It took 2 secs to summarize 1704820 sequences.
mothur > pcr.seqs(fasta=silva.seed_v123.align,start=11894,end=25319,keepdots=F)
Using 1 processors.
Output File Names:
silva.seed_v123.pcr.align
It took 19 secs to screen 14914 sequences.
mothur > system(mv silva.seed_v123.pcr.align silva.v4.fasta)
mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)
Using 1 processors.
Reading in the silva.v4.fasta template sequences... DONE.
It took 5 to read 14914 sequences.
Aligning sequences from stability.trim.contigs.good.unique.fasta ...
It took 298 secs to align 127429 sequences.
Output File Names:
stability.trim.contigs.good.unique.align
stability.trim.contigs.good.unique.align.report
mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 10693 250 0 3 1
2.5%-tile: 1968 11550 252 0 4 42621
25%-tile: 1968 11550 253 0 4 426206
Median: 1968 11550 253 0 5 852411
75%-tile: 1968 11550 253 0 5 1278616
97.5%-tile: 1968 11550 253 0 6 1662200
Maximum: 1982 13383 268 0 10 1704820
Mean: 1968 11550 252.891 0 4.65258
# of unique seqs: 127429
total # of seqs: 1704820
Output File Names:
stability.trim.contigs.good.unique.summary
It took 38 secs to summarize 1704820 sequences.
mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=1968, end=11550, maxhomop=8)
Using 1 processors.
Output File Names:
stability.trim.contigs.good.unique.good.summary
stability.trim.contigs.good.unique.good.align
stability.trim.contigs.good.unique.bad.accnos
stability.trim.contigs.good.good.count_table
It took 44 secs to screen 127429 sequences.
mothur > summary.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.align as input file for the fasta parameter.
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1964 11550 250 0 3 1
2.5%-tile: 1968 11550 252 0 4 42395
25%-tile: 1968 11550 253 0 4 423947
Median: 1968 11550 253 0 5 847893
75%-tile: 1968 11550 253 0 5 1271839
97.5%-tile: 1968 11550 253 0 6 1653391
Maximum: 1968 12070 264 0 8 1695785
Mean: 1968 11550 252.896 0 4.65527
# of unique seqs: 126047
total # of seqs: 1695785
Output File Names:
stability.trim.contigs.good.unique.good.summary
It took 37 secs to summarize 1695785 sequences.
mothur > filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)
Using 1 processors.
Creating Filter...
Running Filter...
Length of filtered alignment: 477
Number of columns removed: 12948
Length of the original alignment: 13425
Number of sequences used to construct filter: 126047
Output File Names:
stability.filter
stability.trim.contigs.good.unique.good.filter.fasta
mothur > unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count_table)
126047 126020
Output File Names:
stability.trim.contigs.good.unique.good.filter.count_table
stability.trim.contigs.good.unique.good.filter.unique.fasta
mothur > pre.cluster(fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.good.unique.good.filter.count_table, diffs=2)
Using 1 processors.
Processing group 120_D1_MB:
11431 2167 9264
Total number of sequences before pre.cluster was 11431.
pre.cluster removed 9264 sequences.
It took 2 secs to cluster 11431 sequences.
Processing group 120_D1_QIA:
4251 657 3594
Total number of sequences before pre.cluster was 4251.
pre.cluster removed 3594 sequences.
It took 0 secs to cluster 4251 sequences.
Processing group 120_D2_MB:
7599 1160 6439
Total number of sequences before pre.cluster was 7599.
pre.cluster removed 6439 sequences.
It took 0 secs to cluster 7599 sequences.
Processing group 120_D2_QIA:
3315 484 2831
Total number of sequences before pre.cluster was 3315.
pre.cluster removed 2831 sequences.
It took 1 secs to cluster 3315 sequences.
Processing group 120_D3_MB:
6365 593 5772
Total number of sequences before pre.cluster was 6365.
pre.cluster removed 5772 sequences.
It took 0 secs to cluster 6365 sequences.
Processing group 120_D3_QIA:
308 98 210
Total number of sequences before pre.cluster was 308.
pre.cluster removed 210 sequences.
It took 0 secs to cluster 308 sequences.
Processing group 120_D4_MB:
3624 314 3310
Total number of sequences before pre.cluster was 3624.
pre.cluster removed 3310 sequences.
It took 0 secs to cluster 3624 sequences.
Processing group 120_D4_QIA:
266 114 152
Total number of sequences before pre.cluster was 266.
pre.cluster removed 152 sequences.
It took 0 secs to cluster 266 sequences.
Processing group 120_D5_MB:
1688 229 1459
Total number of sequences before pre.cluster was 1688.
pre.cluster removed 1459 sequences.
It took 0 secs to cluster 1688 sequences.
Processing group 120_D5_QIA:
37 29 8
Total number of sequences before pre.cluster was 37.
pre.cluster removed 8 sequences.
It took 0 secs to cluster 37 sequences.
Processing group 120_SD_MB:
5583 1368 4215
Total number of sequences before pre.cluster was 5583.
pre.cluster removed 4215 sequences.
It took 1 secs to cluster 5583 sequences.
Processing group 120_SD_QIA:
6803 1044 5759
Total number of sequences before pre.cluster was 6803.
pre.cluster removed 5759 sequences.
It took 0 secs to cluster 6803 sequences.
Processing group 226_D1_MB:
7153 1260 5893
Total number of sequences before pre.cluster was 7153.
pre.cluster removed 5893 sequences.
It took 0 secs to cluster 7153 sequences.
Processing group 226_D1_QIA:
4959 477 4482
Total number of sequences before pre.cluster was 4959.
pre.cluster removed 4482 sequences.
It took 1 secs to cluster 4959 sequences.
Processing group 226_D2_MB:
4801 482 4319
Total number of sequences before pre.cluster was 4801.
pre.cluster removed 4319 sequences.
It took 0 secs to cluster 4801 sequences.
Processing group 226_D2_QIA:
2229 251 1978
Total number of sequences before pre.cluster was 2229.
pre.cluster removed 1978 sequences.
It took 0 secs to cluster 2229 sequences.
Processing group 226_D3_MB:
138 52 86
Total number of sequences before pre.cluster was 138.
pre.cluster removed 86 sequences.
It took 0 secs to cluster 138 sequences.
Processing group 226_D3_QIA:
33 28 5
Total number of sequences before pre.cluster was 33.
pre.cluster removed 5 sequences.
It took 0 secs to cluster 33 sequences.
Processing group 226_D4_MB:
154 64 90
Total number of sequences before pre.cluster was 154.
pre.cluster removed 90 sequences.
It took 0 secs to cluster 154 sequences.
Processing group 226_D4_QIA:
67 32 35
Total number of sequences before pre.cluster was 67.
pre.cluster removed 35 sequences.
It took 0 secs to cluster 67 sequences.
Processing group 226_D5_MB:
Total number of sequences before pre.cluster was 3100.
pre.cluster removed 2780 sequences.
It took 0 secs to cluster 3100 sequences.
Processing group 226_D5_QIA:
26 21 5
Total number of sequences before pre.cluster was 26.
pre.cluster removed 5 sequences.
It took 0 secs to cluster 26 sequences.
Processing group 226_SD_MB:
5987 1316 4671
Total number of sequences before pre.cluster was 5987.
pre.cluster removed 4671 sequences.
It took 0 secs to cluster 5987 sequences.
Processing group 226_SD_QIA:
6516 835 5681
Total number of sequences before pre.cluster was 6516.
pre.cluster removed 5681 sequences.
It took 1 secs to cluster 6516 sequences.
Processing group 294_D1_MB:
8214 1784 6430
Total number of sequences before pre.cluster was 8214.
pre.cluster removed 6430 sequences.
It took 1 secs to cluster 8214 sequences.
Processing group 294_D1_QIA:
5644 837 4807
Total number of sequences before pre.cluster was 5644.
pre.cluster removed 4807 sequences.
It took 0 secs to cluster 5644 sequences.
Processing group 294_D2_MB:
5742 720 5022
Total number of sequences before pre.cluster was 5742.
pre.cluster removed 5022 sequences.
It took 0 secs to cluster 5742 sequences.
Processing group 294_D2_QIA:
3915 424 3491
Total number of sequences before pre.cluster was 3915.
pre.cluster removed 3491 sequences.
It took 0 secs to cluster 3915 sequences.
Processing group 294_D3_MB:
5811 836 4975
Total number of sequences before pre.cluster was 5811.