Error during chimera.vsearch step

Commands in mothur
1

I am having the following error , after removing chimeric sequences after vsearch command.

Removed 1127563 sequences from your fasta file.
[ERROR]: 700463F_697_H7K7TBCX3_2_1101_10000_12021 is not in your count table. Please correct.

I using using latest version Mothur 1.44.0

I have used following scripts

summary.seqs(fasta=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.fasta, count=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.count_table, processors=24)
chimera.vsearch(vsearch=/apps/chpc/bio/mothur/1.44.0//vsearch, fasta=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.fasta, count=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.count_table, dereplicate=t, processors=24)
remove.seqs(fasta=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.fasta, count=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.denovo.vsearch.pick.count_table, accnos=ML_April.trim.contigs.unique.good.pick.good.filter.unique.precluster.denovo.vsearch.accnos)

I am also attaching the mothur log-file for the reference.

Can someone help me out why this error is occuring.

Many thanks

2

Hi guys,

So i am having a new error, during remove.seq command after chimera.vsearch.

Reducing processors to 16.
Error in reading your fastafile, at position -1. Blank name.
It took 4 secs to check 0 sequences.

Removing group: SS1 because all sequences have been removed.
Removing group: SS1A because all sequences have been removed.
Removing group: SS2 because all sequences have been removed.
Removing group: SS2A because all sequences have been removed.
Removing group: SS3 because all sequences have been removed.
Removing group: SS3A because all sequences have been removed.
Removing group: SS4 because all sequences have been removed.
Removing group: SS4A because all sequences have been removed

Any idea, why this particular error is caused.

many thanks
Venkat

3

your first error happens when you get your fasta/count table mismatched -you run some command that removes seqs on one but not the other. go back through your logfile (I don’t see it?) and find that mismatch. Don’t worry about the chimera checking error because it’s likely related.

4

Hi sorry, forget to attach the log file. Here it is one of the recent log file on a new project. i exactly have the same error in remove.seq while using Mothur 1.44.0. I have also tried to remove the particular mismatch sequence from the fasta file. but after removing it is spitting another mismatch. Anyway to workaround this issue would be of very much helpful. Many thanks
Venkat
Mothur logfile

5

There has been a change where flagged chimeras are removed from the count_table in the chimera checking command, so you only need to remove seqs from the fasta.

6

Thanks, Mitchell. I was previously running with 1.39.4 and recently moved to 1.44.0 and i was not aware about these changes.

Now everything works pretty fine.

Many thanks

Venkat

7

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