instaGRAAL on usegalaxy.eu finishes as “ok” but all outputs are 0 bytes

usegalaxy.eu support
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1

Hi!

I am reporting a likely problem with the instaGRAAL tool on usegalaxy.eu.

I ran instaGRAAL (0.1.6+galaxy0) with these inputs:

  • abs_fragments_contacts_weighted.txt

  • fragments_list.txt

  • info_contigs.txt

  • reference genome FASTA

The job ran for about 33 hours and Galaxy marked it as ok, but all 3 output datasets are 0 bytes:

  • Genome sequence

  • Fragment information

  • Curated sequences

In the Job Information page I see:

  • Tool Exit Code = 1

  • Job State = ok

  • Job message:

    • Warning: instaGRAAL is raising an expected error at the end.

    • error_level: 2

    • type: regex

    • stream: stderr

    • match: instagraal_class

This same behaviour happened in two independent histories with different datasets, so it seems systematic and not input-specific.

The output dataset peeks do not contain real FASTA/tabular results, and the datasets remain at 0 bytes even after refresh.

Could you please check whether the Galaxy wrapper is masking a real failure or failing to collect the expected output files?

Thank you.

2

Welcome @alma.wis

Hopefully we can help!

I’m running a simple test on the server right now.

Meanwhile, have you checked the full job logs? This is where to look → FAQ: Troubleshooting errors.

I would also suggest that you send in a bug report from each error job (one dataset from each). You can include a link to this topic in the comments. The administrators of server screen these messages.

You can copy paste the logs back here if you would like to!

More soon as I run my test! :slight_smile:

3

@alma.wis we are aware of this issue with the tool and a few of us have tried to fix it.

Not 100% sure what the latest state is, but obviously things are still not working as they should.

I’m sorry, but I don’t have a better anwer for you at the moment than that this tool is currently unusable and that you may check back here in a few weeks to see if things have changed. I’ll post here when that’s the case.

4

@jennaj marked this as solved to have it show up on the tool interface.