mothur

Chimera.uchime (core dumped) / chimera.vsearch output missing

Hi, I am a new Mothur user, hopefully this isn’t redundant, but I could not find anything especially with this problem by searching the forum.

When I´m running the chimera.uchime command, it´s terminated with the line (core dumped). I don´t think I´m running out of RAM.
chimera.uchime(fasta=work.good.unique.good.filter.unique.precluster.fasta , count=work.good.unique.good.filter.unique.precluster.count_table, dereplicate=t, processors=28)

Because of this issue I was trying to run the dataset with the chimera.vsearch command. This creates only an accnos file. The chimera and the count_table file is missing.

chimera.vsearch(fasta=work.good.unique.good.filter.unique.precluster.fasta, count=work.good.unique.good.filter.unique.precluster.count_table, processors=28)

Thanks!

Welcome to the mothur community! I’d be happy to help.

Because of this issue I was trying to run the dataset with the chimera.vsearch command. This creates only an accnos file. The chimera and the count_table file is missing.

The chimera.vsearch command only creates a count file for you if you run the command with dereplicate=true.

The dereplicate parameter is used to tell mothur how to handle sequences flagged as chimeras across your samples. If the dereplicate parameter is false, then if one group finds the sequence to be chimeric, then all groups find it to be chimeric and the seqeunce is added to the accnos file for removal. If you set dereplicate=t, if a group finds a sequence to be chimeric it is only removed from that group, and mothur creates a modified count file with the chimeric reads removed by sample for you.

Thank you for your help.

The chimera.vsearch creates now a count, accnos and an chimera file.

After this step, I´m running the remove.seqs
remove.seqs(fasta=work.good.unique.good.filter.unique.precluster.fasta, accnos=work.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos)

This deletes 10 sequences and creates a new fasta file called: work.good.unique.good.filter.unique.precluster.pick.fasta

When I now run the summary.seqs I get this following output.
summary.seqs(fasta=work.good.unique.good.filter.unique.precluster.pick.fasta, count=work.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table)

[ERROR]: Your count file contains 1204746 unique sequences, but your fasta file contains 1204736. File mismatch detected, quitting command.

Do I have to delete sequences by hand from the count file ? Isn´t this made by the chimera.vsearch ?
Thanks !

Could you send the work.good.unique.good.filter.unique.precluster.fasta , work.good.unique.good.filter.unique.precluster.count_table, and logfile to mothur.bugs@gmail.com?

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