Hi Folks,
So, I believe some form of this this problem has been address here on the forums before (see here) but I was unable to enact a fix using the recommendations therein. I am hoping someone can perhaps explain it more plainly for me. I am using mothur v1.44.1. I am using vsearch v2.13.3_macos_x86_64.
To explain things from my perspective: I am attempting to process recent MiSeq data using mothur. I am using the MiSeq SOP tutorial as a guideline. I am following the steps precisely as laid out in the SOP and this is the best reference for my inputs to this point.
Even using the files provided by the tutorial, I cannot get past the chimera search, chimera.vsearch(), without error. I believe this is due to a file mismatch, but am not sure. Since I am following a tutorial with sample files I do not suspect poor data to be the culprit.
I have tried a few variations on chimera.vsearch including using fasta+count as the input, as well as fasta+name+group as inputs. The results are the same.
A portion of my log file, including mothur saved files at the time of crash, is posted below (I am not tech-savvy enough to post them as a hyperlink). This screenshot illustrates the fasta read error and subsequent removal of all groups:
Any advice is greatly appreciated! Please let me know if more information/clarification is need! Cheers!
FROM MOTHUR LOGS:
mothur > get.current()
Current RAM usage: 0.327053 Gigabytes. Total Ram: 16 Gigabytes.
Current files saved by mothur:
accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D148.count_table.accnos
fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta
group=/Users/Brad/Desktop/mothur/stability.contigs.good.good.groups
name=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.names
count=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.count_table
processors=4
summary=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.summary
Current default directory saved by mothur: /Users/Brad/Desktop/
Current working directory: /Users/Brad/
Output File Names:
current_files.summary
mothur > chimera.vsearch(fasta=current, name=current, group=current, dereplicate=t)
Using /Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using /Users/Brad/Desktop/mothur/stability.contigs.good.good.groups as input file for the group parameter.
Using /Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.names as input file for the name parameter.
Using 4 processors.
Checking sequences from /Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
/******************************************/
Running command: split.groups(groups=F3D0-F3D1-F3D141-F3D142-F3D143-F3D144-F3D145-F3D146-F3D147-F3D148-F3D149-F3D150-F3D2-F3D3-F3D5-F3D6-F3D7-F3D8-F3D9-Mock, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.count_table)
Using 4 processors.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D6.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D6)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D144.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D144)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D0.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D0)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D149.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D149)
Selected 504 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D144
/******************************************/
Done.
Selected 603 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D6
/******************************************/
Done.
Selected 674 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D0
/******************************************/
Done.
Selected 994 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D149
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D7.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D7)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D145.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D145)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D1.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D1)
/******************************************/
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D150.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D150)
Selected 404 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D7
/******************************************/
Done.
Selected 628 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D145
/******************************************/
Done.
Selected 639 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D150
/******************************************/
Done.
Selected 551 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D1
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D8.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D8)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D146.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D146)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D141.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D141)
/******************************************/
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D2.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D2)
Selected 491 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D8
/******************************************/
Done.
Selected 627 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D146
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D9.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D9)
Selected 531 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D141
/******************************************/
Done.
Selected 1012 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D2
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D142.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D142)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D147.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D147)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D3.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D3)
Selected 622 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D9
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.Mock.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaMock)
Selected 393 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D142
/******************************************/
Done.
Selected 483 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D3
/******************************************/
Done.
Selected 1160 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D147
//
Done.
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D143.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D143)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D5.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D5)
//
Running command: get.seqs(dups=f, accnos=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D148.count_table.accnos, fasta=/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.fastaF3D148)
Selected 133 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaMock
/******************************************/
Done.
Selected 407 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D143
/******************************************/
Done.
Selected 471 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D5
/******************************************/
Done.
Selected 901 sequences from your fasta file.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fastaF3D148
/******************************************/
Done.
Output File Names:
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D0.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D0.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D1.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D1.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D141.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D141.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D142.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D142.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D143.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D143.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D144.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D144.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D145.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D145.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D146.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D146.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D147.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D147.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D148.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D148.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D149.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D149.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D150.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D150.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D2.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D2.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D3.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D3.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D5.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D5.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D6.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D6.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D7.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D7.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D8.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D8.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.F3D9.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.F3D9.fasta
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.Mock.count_table
/Users/Brad/Desktop/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.Mock.fasta