Non zero exit status

[mdehollander]

Since we moved to a new server running Ubuntu 16.04, I got the sina binary from here (1.3.1-a5). The programs runs fine and produces output, but when I integrate it in Snakemake it complains that it returns a non-zero exit status 6. And therefore it removes the output files. Any idea why it doesn't give a 0 exit code?

[epruesse]

Exit code 6 is IIRC "invalid file handle". What does the log say? My best guess is that this is due to the logging subsystem trying to open /dev/stderr and failing. Try adding log: {bla}.log and --log-file {log} to your rule.

[epruesse]

@mdehollander Did you figure out what was going on?

[mdehollander]

I had a look again and now used the latest version from bioconda. Now I get a 141 exit code when I run it directly, not in a snakemake rule (with snakemake it also still fails). This is the command I use.

$ sina --log-file sina.log -i test.fasta --intype fasta -o sina.align \
   --outtype fasta --meta-fmt csv \
   --ptdb /data/db/Silva/128/SSURef_NR99_128_SILVA_07_09_16_opt.arb \
   --overhang remove --turn all --search \
   --search-db /data/db/Silva/128/SSURef_NR99_128_SILVA_07_09_16_opt.arb \
   --search-min-sim 0.95 --search-no-fast --search-kmer-len 10 --lca-fields tax_slv

$ echo $?
141

The complete output can be seen at https://paste.ubuntu.com/25124176/

Could it be that there is a filehandle still open and that it complains that sina stops without closing it?

[epruesse]

141 is SIGPIPE. Probably because SINA tried to read from the pipe coming from the PT server when that process was already terminated. So a bug in the handling of the background process shutdown. Looking at the log, SINA completed its run though. You should have sequences in the output and a log to show that it worked.

I'm not certain how much work I want to invest into the PT server handling. I've got an internal kmer search half ready that would replace it and should be faster anyway.

[mdehollander]

The output is indeed there and looks fine. I managed to force a 0 exit code by adding || : to the end of the line. Not really elegant, but it works. Wouldn't invest to much time in it, improvements like a kmer search or multiprocessing are more useful time investments I would say.

[epruesse]

|| true is a more obvious way of saying "exit code ignored". If you add a 2> sina.errorlog you can then check for crashes with grep -q "SINA finished." sina.errorlog. Not perfect, but it'll do.