Trim.seqs command issues

Commands in mothur
1

Hello All,

Following the 454 SOP, I have some trouble with the command “trim.seqs”
When I type:
“trim.seqs(fasta=Contigs.fasta, qfile=Contigs.qual, qaverage=20, maxambig=0, maxhomop=8, minlength=300, maxlength=350, processors=12)”

The output returned is:
sequence name mismatch btwn fasta:M00707_53_000000000_AG56W_1_2113_24554_18471 _and qual file:M00707_53_000000000_AG56W_1_260373"
…
I was using the lastest of version.
Any thoughts on how to resolve this issue? Thank you very much!

2

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3

Could the files could have sequences in different orders? You can test that by using the sort.seqs command, https://www.mothur.org/wiki/Sort.seqs.

mothur > sort.seqs(fasta=Contigs.fasta, qfile=Contigs.qual)