bin/lib/kofam_scan/parallel.rb:28:in `write': Broken pipe (Errno::EPIPE) about kofam_scan

[takaram]

Hmm... sorry I have no idea about the error. Do you get it every time? Do you run more than one KofamScan in parallel?

[PandengWang]

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

[achmall]

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)
`

[PandengWang]

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