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chloroExtractorTeam / chloroExtractor

MIT License
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PipeWrap error after jellyfish #22

Closed iimog closed 6 years ago

iimog commented 6 years ago

When starting ptx.pl on some Arabidopsis example data I get the following output:

$ bin/ptx --config ptx.cfg -1 ERR2026804_2.5M_1.fastq -2 ERR2026804_2.5M_2.fastq -o out -d test_ara
[17-08-15 13:04:27] [PipeWrap] Running 'jf0': jellyfish count -t 8 -m 31 -s 500M -C -o jf0.jf /projects/chloroExtractor/ERR2026804_2.5M_1.fastq /projects/chloroExtractor/ERR2026804_2.5M_2.fastq
can't create : No such file or directory at /projects/chloroExtractor/bin/../lib/PipeWrap.pm line 267.

Looks like jellyfish is running fine and PipeWrap can not create the trace file.

iimog commented 6 years ago

It looks that $trace_file is not properly set in PipeWrap because hard-coding the default value from undef to '/tmp/trace' avoids this problem. Although this is obviously not the perfect fix.

PfaffS commented 6 years ago

You're right, the $trace_file is set to undef (i think we've done this because it was in Thomas version also set to undef), but he set it afterwards to "ID".trace if nothing is set. it seems we forgot to do that, so we have two options: first: We set the trace_file in the ptx.cfg or second: everytime no trace_file is set I just set it also to "ID".trace - i think option two is the better way to fix this

greatfireball commented 6 years ago

The error message is not helpful, It just states Can't create :, was a desperate issue.

It is till not solved