Closed g-pacheco closed 2 years ago
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
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.
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
Thanks a lot, Mikkel. Have a great evening!
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
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.
Dear @MikkelSchubert,
I am trying to run PaleoMix v2.0.0a0 but I am getting an error when trying to enter a BED file:
The dryrun runs normally when I comment the two
RegionsOfInterest
lines:I am attaching here my
.YAML
and my.BED
files.PaleoMixFiles.zip
Any ideas of what could be happening? I reckon I am overlooking something but I cannot really tell what that would be.
Many thanks in advance, George.