Error after running "count.seqs" command

Commands in mothur
1

I am getting these unusual errors after the “count.seqs” command :
“…
[ERROR]: HRBQ4LI01CP2LW is not in your groupfile, please correct.
[ERROR]: HRNL7LJ02HEHWU is not in your groupfile, please correct.
[ERROR]: HRBQ4LI01BLQXO is not in your groupfile, please correct.
[ERROR]: HRNL7LJ02HZXMY is not in your groupfile, please correct.
[ERROR]: HRI6PBN02GRKWU is not in your groupfile, please correct.
[ERROR]: HQRGCMO01CUPES is not in your groupfile, please correct.
[ERROR]: HRNL7LJ02IDEXH is not in your groupfile, please correct.
[ERROR]: HRNL7LJ02IQCXM is not in your groupfile, please correct.
[ERROR]: HTFXETZ01CPNHE is not in your groupfile, please correct.
[ERROR]: HTFXETZ02JD5UM is not in your groupfile, please correct.
[ERROR]: HTFXETZ01AO0HQ is not in your groupfile, please correct.
[ERROR]: processes reported processing 20950579 sequences, but group file indicates you have 20835900 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.”

I am not able to understand the error and I am not even getting any solutions from the internet. It would be helpful if someone could provide some insight into this :slight_smile:

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2

Hi,

THis generally happens because you’re using the wrong files - if sequences have been removed from one file but not the other. Can you post the exact commands you are running upstream of this?

Pat

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3

These were the commands that I had used :

">>make.contigs(file=mothur-data1/data1.files, processors=120)

summary.seqs(fasta=mothur-data1/data1.trim.contigs.fasta, processors=120)
screen.seqs(fasta=mothur-data1/data1.trim.contigs.fasta, group=mothur-data1/data1.contigs.groups, summary=mothur-data1/data1.trim.contigs.summary, maxambig=0, maxlength=500)
get.current() #current_files.summary
unique.seqs(fasta=current)
count.seqs(name=current, group=current)"

Thanks

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4

Can we check to see where the files mismatched? Try this:

mothur > make.contigs(file=mothur-data1/data1.files, processors=120)
mothur > summary.seqs(fasta=current)
mothur > count.groups(group=current)

Do the number of sequences in each file match here?

mothur > screen.seqs(fasta=mothur-data1/data1.trim.contigs.fasta, group=mothur-data1/data1.contigs.groups, summary=mothur-data1/data1.trim.contigs.summary, maxambig=0, maxlength=500)
mothur > summary.seqs(fasta=current)
mothur > count.groups(group=current)

Do the number of sequences in each file match here?

You don’t have to rerun the make.contigs and screen.seqs commands if you want to just run the output files through the summary and count commands.

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