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just annotate it, dammit!
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1.0 Backport hmmscan issue #83

Open macmanes opened 7 years ago

macmanes commented 7 years ago

Having an issue with the hmmscan part of the run

Some tasks failed![dammit.annotate:ERROR]
TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR]
Command error: 'cat good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep | /usr/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 36 -a good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep /opt/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out /home/lauren/Documents/Nov2016Dammit/dammit/Pfam-A.hmm /dev/stdin > good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl' returned 255
[dammit.annotate:ERROR]

when running this command on its own you see this error:

cat good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep \
| /usr/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 36 -a good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep \
/opt/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 \
-o good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out \
/home/lauren/Documents/Nov2016Dammit/dammit/Pfam-A.hmm /dev/stdin \
> good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl

parallel: Error: Command line too long (49809910 >= 131071) at number -2: ...

FYI, parallel version is GNU parallel 20141022. I could get version 20160922 from LinuxBrew if you think that older version is the issue.

camillescott commented 7 years ago

Bleh, yeah, it needs the newer version. Forgot to add the version check for GNU parallel into the backport release.

On Wed, Nov 30, 2016 at 5:18 PM, Matt MacManes notifications@github.com wrote:

Having an issue with the hmmscan part of the run

Some tasks failed![dammit.annotate:ERROR] TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR] Command error: 'cat good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep | /usr/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 36 -a good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep /opt/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out /home/lauren/Documents/Nov2016Dammit/dammit/Pfam-A.hmm /dev/stdin > good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl' returned 255 [dammit.annotate:ERROR]

when running this command on its own you see this error:

cat good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep \ | /usr/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 36 -a good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep \ /opt/hmmer-3.1b2-linux-intel-x86_64/binaries/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 \ -o good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl.out \ /home/lauren/Documents/Nov2016Dammit/dammit/Pfam-A.hmm /dev/stdin \

good.BINPACKER.cdhit.fasta.transdecoder_dir/longest_orfs.pep.pfam.tbl

parallel: Error: Command line too long (49809910 >= 131071) at number -2: ...

FYI, parallel version is GNU parallel 20141022. I could get version 20160922 from LinuxBrew if you think that older version is the issue.

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-- Camille Scott

Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis

camille.scott.w@gmail.com