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a-h-b / binny

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Prokka's file writing problem #62

Closed Andyargueasae closed 1 week ago

Andyargueasae commented 2 weeks ago

Hi,

It is so weird that this error today popped out for gene annotation. The job of annotate cannot pass, here is the log information I had.

2024-09-18T164353.446228.snakemake.log

And I then checked the log information of annotate rule, everything looks fine, and the output is already there, with exit code as 0. analysis_annotate.log

Andyargueasae commented 2 weeks ago

A further investigation gives such error message when running prokka:

------------- EXCEPTION ------------- MSG: Could not write file '/data/chloroscan/binny_output/intermediary/prokka.faa': No such file or directory STACK Bio::Root::IO::_initialize_io /home/student.unimelb.edu.au/yuhtong/mambaforge/envs/prokkaenv/lib/perl5/site_perl/Bio/Root/IO.pm:272 STACK Bio::SeqIO::_initialize /home/student.unimelb.edu.au/yuhtong/mambaforge/envs/prokkaenv/lib/perl5/site_perl/Bio/SeqIO.pm:508 STACK Bio::SeqIO::fasta::_initialize /home/student.unimelb.edu.au/yuhtong/mambaforge/envs/prokkaenv/lib/perl5/site_perl/Bio/SeqIO/fasta.pm:88 STACK Bio::SeqIO::new /home/student.unimelb.edu.au/yuhtong/mambaforge/envs/prokkaenv/lib/perl5/site_perl/Bio/SeqIO.pm:384 STACK Bio::SeqIO::new /home/student.unimelb.edu.au/yuhtong/mambaforge/envs/prokkaenv/lib/perl5/siteperl/Bio/SeqIO.pm:430 STACK toplevel /data/chloroscan/conda/7a9f0871ba17c37c7fea5f02871f8ff6/lib/binny_Chloroscan/workflow/bin/prokkaP:1414

ohickl commented 1 week ago

Hi Andy, did you find a solution? Maybe you ran out of space/file writing quota?

Best Oskar

Andyargueasae commented 1 week ago

Yes. And after that I closed that issue.

My bad，the version of system python has conflicts with snakemake.

And now no more worries.

Andy

Oskar Hickl @.***>于2024年9月20日 周五17:22写道：

Hi Andy, did you find a solution? Maybe you ran out of space/file writing quota?

Best Oskar

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