Closed davidvilanova closed 5 years ago
Thanks for reporting this issue.
Could you please provide the command line that you used to dereplicate the sequences with vsearch as well?
The problem seems to be caused by the space in the header line after "ech97_125". Swarm will interpret this as the end of the identifier. It will not find an abundance value in the expected format (;size=
), because the -z
option was given, and therefore complain. The abundance of 9503 computed by vsearch is ignored.
Usually vsearch will drop the part of the header after the space, but I think it may include it when converting directly from FASTQ.
Oh i see, Here is the command line:
vsearch --derep_fulllength Sequences.fa.gz --output $outdir/derep.fa --uc=$outdir/derepuc.uc --log=$outdir/log.derep --minuniquesize 1 --fasta_width 0 --sizeout
The input file is a fasta file, containing the space. I can remove everything after the space and keep the ;size=INT
For intance if it change the header to >ech97_125;size=9503
it should work ?
I´ve used awk to clean headers on derep.fa
awk -F'[ :;]' '{print $1,$NF}' OFS=";" $outdir/derep.fa
Probably should have cleaned headers early on....
Thanks.
For intance if it change the header to >ech97_125;size=9503 it should work ?
Yes, that should work.
Unfortunately, there seems to be an issue with the derep_fulllength
command in VSEARCH. It fails to remove everything in the header starting with the space. That's a bug. Sorry for that. I'll fix it.
I´ve used awk to clean headers on derep.fa
awk -F'[ :;]' '{print $1,$NF}' OFS=";" $outdir/derep.fa
or sed -i '/^>/ s/ .*;size=/;size=/' file.fas
Thanks for reporting that issue @davidvilanova
The issue in vsearch: https://github.com/torognes/vsearch/issues/338
Thanks guys for quick response !!!
The bug is fixed in vsearch 2.8.6, just released.
Hi, While using swarm on dereplicated seqs using vsearch i got the following error
Vsearch output Looks fine
swarm output
swarm -f -t 3 -d 1 -z $outdir/derep.fa -s $outdir/amplicons.stats -u $outdir/ucfinal.txt -w $outdir/OTUs_temp.fa -l $outdir/logswarm > $outdir/amplicons.swarms
The dereplicated file (derep.fa). This is the first sequence of the file
Using vsearch v2.8.5_linux_x86_64 and Swarm 2.2.2 [Jun 21 2018 17:48:50] on linux.