Closed tbenavi1 closed 9 months ago
kcleal
commented
9 months ago 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!
kcleal
commented
9 months ago 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.
tbenavi1
commented
9 months ago Thank you. I will take a look and see if this fixes my issue.
tbenavi1
commented
9 months ago Hello, I installed the dev branch (commit 04eb5d1e7795ab2e27e1dd9a9e52baf2afee7cf7), 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 rangeFor 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.vcfAnd 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 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
kcleal
commented
9 months ago 1.6.1 should be available tomorrow from pypi, if you don't mind waiting
Hello I ran the dysgu filter command and got the following error:
Any advice? Let me know if you need further information from me. Thanks.