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MikkelSchubert avatar MikkelSchubert commented on July 29, 2024 1

Well, that's not supposed to happen. Thanks for letting me know! I'll try to publish a fix tomorrow.

In the mean time, you should still be able to get coverage/summary statistics if you temporarily disable the Depths feature.

Best,
Mikkel

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MikkelSchubert avatar MikkelSchubert commented on July 29, 2024 1

I've now released a new version of PALEOMIX that should hopefully fix the problem (v1.3.7).
Let me know if you run into any other issues.

Best, Mikkel

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MikkelSchubert avatar MikkelSchubert commented on July 29, 2024

Hi George,

Paleomix v2.0.0a0 is currently not in a state where I'd recommend it for general use (the a is for alpha).
More specifically, support for regions of interest have been removed temporarily (along with coverage, depth, and summary statistics), since I intend to rework those features when I have time.

So unless you need specific functionality that is only in the development branch, then I'd recommend that you use the latest release, namely v1.3.6.

Best,
Mikkel

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g-pacheco avatar g-pacheco commented on July 29, 2024

Hello @MikkelSchubert,

Thanks very much for your swift reply.

Oh, sorry. I gave you the error from v2.0.0a0 because I thought that would be preferable -- my bad. I also get an error when I try to run v1.3.6 with a .BED file -- here it is:

paleomix bam dryrun --max-threads 2 --adapterremoval-max-threads 2 --bwa-max-threads 2 --log-level info --log-file UkData_PaleoMix.log UKData_PaleoMix.yaml
16:49:55 INFO Reading makefile 'UKData_PaleoMix.yaml'
16:49:55 INFO Validating FASTA files
16:49:55 INFO Building BAM pipeline for 'UKData_PaleoMix.yaml'
Traceback (most recent call last):
  File "/projects/mjolnir1/apps/conda/paleomix/bin/paleomix", line 8, in <module>
    sys.exit(entry_point())
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/main.py", line 118, in entry_point
    return main(sys.argv[1:])
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/main.py", line 114, in main
    return module.main(argv[1:])
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/pipelines/bam/pipeline.py", line 255, in main
    return run(args, pipeline_variant=pipeline)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/pipelines/bam/pipeline.py", line 208, in run
    nodes = pipeline_func(config, makefile)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/pipelines/bam/pipeline.py", line 120, in build_pipeline_full
    parts.add_statistics_nodes(config, makefile, target)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/pipelines/bam/parts/statistics.py", line 37, in add_statistics_nodes
    nodes.extend(_build_depth(config, target, makefile["Prefixes"]))
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/pipelines/bam/parts/statistics.py", line 74, in _build_depth
    DepthHistogramNode(
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/nodes/commands.py", line 112, in __init__
    command=builder.finalize(),
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/atomiccmd/builder.py", line 227, in finalize
    self._object = AtomicCmd(self.call, **self.kwargs)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/atomiccmd/command.py", line 143, in __init__
    arguments = self._process_arguments(id(self), self._command, kwargs)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/atomiccmd/command.py", line 329, in _process_arguments
    cls._validate_arguments(arguments)
  File "/projects/mjolnir1/apps/conda/paleomix/lib/python3.9/site-packages/paleomix/atomiccmd/command.py", line 380, in _validate_arguments
    raise ValueError(
ValueError: TEMP_IN_INDEX cannot contain dir component: './Manchester_01.RockDove_DoveTail_ReRun.bam.bai'

Please let me know should you need any other information.

Kind regards, George.

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g-pacheco avatar g-pacheco commented on July 29, 2024

Thanks a lot, Mikkel.
Have a great evening!

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g-pacheco avatar g-pacheco commented on July 29, 2024

Hello Mikkel,

Thanks a lot for acting on this so quickly. I am glad to confirm that this new version did fix the problem.

Greetings from Silkeborg, George.

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