This is Jake Lee at Memorial Sloan Kettering Cancer Center. First of all, thank you so much for developing this wonderful tool. I would love to try the recently added copy number feature, so tried a couple of attempts during this weekend after re-installing SAVANA. I would like to troubleshoot my errors under your guidance if possible. Previously I used version 1.0.5, which showed good performance in calling SVs. Now I am using the version 1.2.0. For the phased_vcf, I used my vcf file generated from deepvariant-margin-whatshap pipeline. My reference genome is chm13v2.0 (T2T).
First, I tried to run "savana cna" based on the previous breakpoint.vcf file from version 1.0.5 ("somatic.classified.breakpoint.vcf"). But I got this error message below:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/site-packages/savana/read_counter.py", line 59, in binned_read_counting
blacklist = float(bin[4])
File "pybedtools/cbedtools.pyx", line 524, in pybedtools.cbedtools.Interval.__getitem__
IndexError: field index out of range
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/bin/savana", line 8, in <module>
sys.exit(main())
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/site-packages/savana/savana.py", line 496, in main
args.func(args)
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/site-packages/savana/savana.py", line 201, in savana_cna
read_counts_path = read_counter.count_reads(outdir, args.tumour, args.normal, args.panel_of_normals, args.sample, bin_annotations_path, args.readcount_mapq, args.blacklisting, args.bl_threshold, args.bases_filter, args.bases_threshold, args.threads)
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/site-packages/savana/read_counter.py", line 176, in count_reads
countData = [x for xs in list(pool.starmap(binned_read_counting, args_in)) for x in xs]
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/multiprocessing/pool.py", line 372, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/data1/shahs3/users/leej39/environment/miniconda3/envs/savana_env/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
IndexError: field index out of range
I also tried running the new savana 1.2.0 from the scratch, by calling SVs again and analyzing CNAs, but it also gives me the exact same error message. In terms of the output files, I see that 10kbp_bin_ref...bed file is generated. The last part of the output file is as below.
Hi Jake, thank you for your comment! Please could you share some more detail on how exactly you are running savana cna? Are you providing a blacklist and which flags have you specified/used?
Thank you!
Carolin
Hi colleagues,
This is Jake Lee at Memorial Sloan Kettering Cancer Center. First of all, thank you so much for developing this wonderful tool. I would love to try the recently added copy number feature, so tried a couple of attempts during this weekend after re-installing SAVANA. I would like to troubleshoot my errors under your guidance if possible. Previously I used version 1.0.5, which showed good performance in calling SVs. Now I am using the version 1.2.0. For the phased_vcf, I used my vcf file generated from deepvariant-margin-whatshap pipeline. My reference genome is chm13v2.0 (T2T).
First, I tried to run "savana cna" based on the previous breakpoint.vcf file from version 1.0.5 ("somatic.classified.breakpoint.vcf"). But I got this error message below:
I also tried running the new savana 1.2.0 from the scratch, by calling SVs again and analyzing CNAs, but it also gives me the exact same error message. In terms of the output files, I see that 10kbp_bin_ref...bed file is generated. The last part of the output file is as below.
Any thoughts how I could fix this error will be greatly appreciated!
Best,
Jake June-Koo Lee, MD, PhD