Comments (6)
kcleal
commented on June 12, 2024
1
1.6.1 should be available tomorrow from pypi, if you don't mind waiting
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kcleal
commented on June 12, 2024
Hi @tbenavi1,
Thanks for reporting this. It looks like a simple index error which should be easy for me to fix. I will take a look today. Would you mind sharing the upstream commands you used for calling and filtering, just for me to check if there it anything else in it? Also could you confirm which version of dysgu you are using, thanks!
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kcleal
commented on June 12, 2024
Ive added a fix to the dysgu_dev branch on github https://github.com/kcleal/dysgu/tree/dysgu_dev. You will have to build dysgu from source whilst I finish some other changes being made to version 1.6.1. This can be done by cloning the dev_branch and running the INSTALL.sh script.
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tbenavi1
commented on June 12, 2024
Thank you. I will take a look and see if this fixes my issue.
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tbenavi1
commented on June 12, 2024
Hello, I installed the dev branch (commit 04eb5d1), but I still have the issue. I ran with the same file and got:
Traceback (most recent call last):
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/bin/dysgu", line 33, in <module>
sys.exit(load_entry_point('dysgu==1.6.1', 'console_scripts', 'dysgu')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/main.py", line 467, in filter_normal
filter_normals.run_filtering(ctx.obj)
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/filter_normals.py", line 907, in run_filtering
good = process_intra(r, posB, bams, infile, bam_is_paired_end, support_fraction, pad=pad, sample=sample_name, keep_all=keep_all)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/filter_normals.py", line 829, in process_intra
if cached and matching_soft_clips(r, cached, is_paired_end):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/filter_normals.py", line 594, in matching_soft_clips
break_seqs = BreakSeqs(r)
^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/filter_normals.py", line 287, in __init__
left_clip, right_clip = get_contig_clipped_bases(r.info["CONTIGA"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rranallo-benavidez/mambaforge/envs/snakemake/lib/python3.11/site-packages/dysgu/filter_normals.py", line 264, in get_contig_clipped_bases
while cont[i].islower():
~~~~^^^
IndexError: string index out of range
For reference, the filter command I ran was
dysgu filter --normal-vcf results/dysgu/NHA_p1/NHA_p1.svs.vcf -p 32 results/dysgu/NHA_E6E7_D12_PDL50/NHA_E6E7_D12_PDL50.svs.vcf results/BAMS/NHA_p1/T2T.NHA_p1.sorted.bam > results/dysgu/NHA_E6E7_D12_PDL50/NHA_E6E7_D12_PDL50.somatic.vcf
And the call command I ran was:
dysgu call --mode nanopore --mq 20 --overwrite -p 32 {input.ref} {params.tmp} {input.bam} > results/dysgu/NHA_E6E7_D12_PDL50/NHA_E6E7_D12_PDL50.svs.vcf
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kcleal
commented on June 12, 2024
Hi @tbenavi1,
I think you might be accidentally using the master branch still. Line 264 in filter_normals.py has been changed on the Dev branch. https://github.com/kcleal/dysgu/blob/dysgu_dev/dysgu/filter_normals.py#L264
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