Hi,
I’m following the Miseq SOP to the letter, and after I perform unique.seqs (which seems to work OK), I get a problem:
mothur > count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
Using 16 processors.
[ERROR]: processes reported processing 1068690 sequences, but group file indicates you have 1068725 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.
I’d appreciate a fix…
P.
/// Here is the full logfile:
Windows version
Running 64Bit Version
mothur v.1.33.3
Last updated: 4/4/2014
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
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
Type ‘quit()’ to exit program
Interactive Mode
mothur > make.contigs(file=stability.files, processors=16)
Using 16 processors.
Reading fastq data…
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Done.
Processing MB01_CACGAGATGA_L001_R1_001.0ffastatemp (file 1 of 20) <<<<<
Making contigs…
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Processing MB02_ACGCACATAT_L001_R1_001.0ffastatemp (file 2 of 20) <<<<<
Making contigs…
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Processing MB03_ACGTGCTCTG_L001_R1_001.0ffastatemp (file 3 of 20) <<<<<
Making contigs…
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Processing MB04_ACGATCACAT_L001_R1_001.0ffastatemp (file 4 of 20) <<<<<
Making contigs…
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Processing MB05_AGTGTACTCA_L001_R1_001.0ffastatemp (file 5 of 20) <<<<<
Making contigs…
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Processing MB11_TGATGTATGT_L001_R1_001.0ffastatemp (file 6 of 20) <<<<<
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Processing MB12_GATATATGTC_L001_R1_001.0ffastatemp (file 7 of 20) <<<<<
Making contigs…
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Processing MB13_TAGTACTAGA_L001_R1_001.0ffastatemp (file 8 of 20) <<<<<
Making contigs…
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Processing MB14_TATAGAGATC_L001_R1_001.0ffastatemp (file 9 of 20) <<<<<
Making contigs…
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Processing MB15_TCGATATCTA_L001_R1_001.0ffastatemp (file 10 of 20) <<<<<
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Processing MB21_TACATGATAG_L001_R1_001.0ffastatemp (file 11 of 20) <<<<<
Making contigs…
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Processing MB22_TGAGATCATA_L001_R1_001.0ffastatemp (file 12 of 20) <<<<<
Making contigs…
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Processing MB23_CTACATACTA_L001_R1_001.0ffastatemp (file 13 of 20) <<<<<
Making contigs…
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Processing MB24_ATCAGTGTAT_L001_R1_001.0ffastatemp (file 14 of 20) <<<<<
Making contigs…
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Processing MB25_ATCATATCTC_L001_R1_001.0ffastatemp (file 15 of 20) <<<<<
Making contigs…
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Processing MB26_AGTAGATCAT_L001_R1_001.0ffastatemp (file 16 of 20) <<<<<
Making contigs…
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Processing MB27_ACATAGTATC_L001_R1_001.0ffastatemp (file 17 of 20) <<<<<
Making contigs…
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Processing MB28_ATGTATAGTC_L001_R1_001.0ffastatemp (file 18 of 20) <<<<<
Making contigs…
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Processing MB29_ACAGTCATAT_L001_R1_001.0ffastatemp (file 19 of 20) <<<<<
Making contigs…
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Processing MB38_ACATATACGT_L001_R1_001.0ffastatemp (file 20 of 20) <<<<<
Making contigs…
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Done. It took 752 secs to process 1241833 sequences.
Group count:
MB01 55872
MB02 54715
MB03 54618
MB04 75092
MB05 87781
MB11 77916
MB12 64309
MB13 73444
MB14 54165
MB15 60464
MB21 62489
MB22 60187
MB23 83380
MB24 70636
MB25 89720
MB26 33103
MB27 57895
MB28 52647
MB29 73360
MB38 40
Total of all groups is 1241833
Output File Names:
stability.trim.contigs.fasta
stability.contigs.report
stability.scrap.contigs.fasta
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 16 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 295 295 0 3 1
2.5%-tile: 1 308 308 0 4 31045
25%-tile: 1 308 308 0 4 310450
Median: 1 308 308 0 6 620900
75%-tile: 1 308 308 0 6 931349
97.5%-tile: 1 309 309 6 6 1210754
Maximum: 1 601 600 117 298 1241798
Mean: 1 309.256 309.256 0.500144 5.35128
of Seqs: 1241798
Output File Names:
stability.trim.contigs.summary
mothur > screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=320)
Using 16 processors.
Output File Names:
stability.trim.contigs.good.fasta
stability.trim.contigs.bad.accnos
stability.contigs.good.groups
It took 27 secs to screen 1241798 sequences.
mothur > unique.seqs(fasta=stability.trim.contigs.good.fasta)
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1068690 464011
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 16 processors.
[ERROR]: processes reported processing 1068690 sequences, but group file indicates you have 1068725 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.