Comments (6)
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
from paleomix.
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
from paleomix.
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
from paleomix.
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.
from paleomix.
Thanks a lot, Mikkel.
Have a great evening!
from paleomix.
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.
from paleomix.
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