Comments (4)
Hmm... sorry I have no idea about the error. Do you get it every time? Do you run more than one KofamScan in parallel?
from kofam_scan.
Hmm... sorry I have no idea about the error. Do you get it every time? Do you run more than one KofamScan in parallel?
Yes, I encountered this error every time when I annotated my whole protein seqs (16762174).
But, when I used a subset of the protein seqs, such as 200, it didn't report this error.
The comment I run: exec_annotation -o y19-all15_prot_kegg.annotations ../4.genePrediction/y19-all15_prot_catalogue_relabel.faa -p /software/xxx/kegg/kofam/profiles/ -k /software/xxx/kegg/kofam/ko_list --cpu=1 --tmp-dir=/mdata/xxx/tmp -f mapper-one-line --no-report-unannotated
from kofam_scan.
I get the same error when trying to run kofamscan on a server, whereas it is working fine with the same input file on my local machine...
$ ./exec_annotation -o 26052020_kofamscan_HACON.txt /export/work_cgb/Achim/HACON_sequencing/200408_K00253.A.Project_Mall-DNA1-2020-02-13/gene_calls_aa.fa Traceback (most recent call last): 10: from ./exec_annotation:7:in
9: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/cli.rb:21:in
run' 8: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/executor.rb:8:in
execute'7: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/executor.rb:35:in
execute' 6: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/executor.rb:107:in
run_hmmsearch'5: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/parallel.rb:27:in
exec' 4: from /export/home/sey013/.conda/envs/kofamscan/lib/ruby/2.6.0/open3.rb:101:in
popen3'3: from /export/home/sey013/.conda/envs/kofamscan/lib/ruby/2.6.0/open3.rb:219:in
popen_run' 2: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/parallel.rb:28:in
block in exec'1: from /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/parallel.rb:28:in
puts' /export/work_cgb/Achim/kofam_scan/lib/kofam_scan/parallel.rb:28:in
write': Broken pipe (Errno::EPIPE)`
from kofam_scan.
Hi All,
I may have figured out the reason underlying this error.
This error come from Linux parallel
command, which is called in exec_annotation
.
When you close your shell window, the Linux parallel
will recieve signal and won't submit new jobs, even you run parallel
with nohup
.
One possible method to resolve this issue is that after you run exec_annotation
with nohup
in the backgroud, you could disconnect this command with your current shell using disown -h %jobid
or disown -a
.
Hope this message will help you guy who have encountered the same error.
Pandeng
from kofam_scan.
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from kofam_scan.