CNVkit segment command RuntimeError: Subprocess command failed

[tanbiswas]

I am using CNVkit to call somatic CNAs from tumor-normal paired WES data. The BAM files were generated using GATK pipeline and the somatic VCF file was called using Mutect2 pipeline. However, I am getting the following error while running cnvkit segmentation command.

(cnvkit) iit@lab:/P03-TD$ cnvkit.py segment P03-TD.cnr -o P03-TD.cns -m cbs --smooth-cbs --vcf P03.somatic.vcf --sample-id P03-TD --normal-id P03-BD --min-variant-depth 10
Selected test sample P03-TD and control sample P03-BD
Loaded 3536 records; skipped: 0 somatic, 9 depth
VCF normal sample's genotypes are all 0/0 or missing; inferring genotypes from allele frequency instead
Skipping 99 additional somatic records based on T/N genotypes
Kept 31 heterozygous of 3437 VCF records
Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Re-segmenting on variant allele frequency
.
.
Re-segmenting on variant allele frequency
Traceback (most recent call last):
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/core.py", line 23, in call_quiet
proc = subprocess.run(args, check=True, capture_output=True)
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('Rscript', '--no-restore', '--no-environ', '/tmp/tmpgodv9oax')' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/iit/miniconda3/envs/cnvkit/bin/cnvkit.py", line 10, in
sys.exit(main())
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/commands.py", line 1022, in _cmd_segment
results = segmentation.do_segmentation(
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 81, in do_segmentation
rets = list(
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 126, in _ds
return _do_segmentation(*args)
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/init.py", line 209, in _do_segmentation
seg_out = core.call_quiet(
File "/home/iit/miniconda3/envs/cnvkit/lib/python3.10/site-packages/cnvlib/core.py", line 30, in call_quiet
raise RuntimeError(
RuntimeError: Subprocess command failed:
$ Rscript --no-restore --no-environ /tmp/tmpgodv9oax

Command '('Rscript', '--no-restore', '--no-environ', '/tmp/tmpgodv9oax')' returned non-zero exit status 1.
(cnvkit) iit@lab:P03-TD$

I have tried many ways but still getting this error. R package 'DNACopy' is successfully installed in my system.

Please let me know how to solve this!

[bounlu]

Everybody gets the same error and this is still not solved: nf-core/sarek#1625

[etal]

In P03-TD.cnr, is the weight column empty, or does it have some empty cells along with numeric values?

[etal]

Related: #436

[etal]

I merged a possible fix in #914. Could you try pulling the latest development version and see if the problem is fixed now?

[jezkoski]

I have the same issue and I'm using the latest version from github (0.9.12).