Open bounlu opened 3 weeks ago
Please provde your command and respective log files ( in this case the .command.sh
of a cnvkit process would also be useful) to investigate. This is not a general issue, since these files are clearly generated in the full size tests https://nf-co.re/sarek/3.4.3/results/sarek/results-e92242ead3dff8e24e13adbbd81bfbc0b6862e4c/test_full_aws/variant_calling/cnvkit/HCC1395T_vs_HCC1395N/
When I cd to the work directory and run the segment
command, it fails as below:
$ docker run --rm -it -v /data:/data quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0
$ cnvkit.py segment my_sample.cnr -o my_sample.cns
Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Traceback (most recent call last):
File "/usr/local/bin/cnvkit.py", line 10, in <module>
sys.exit(main())
File "/usr/local/lib/python3.10/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "/usr/local/lib/python3.10/site-packages/cnvlib/commands.py", line 994, in _cmd_segment
results = segmentation.do_segmentation(
File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 79, in do_segmentation
rets = list(
File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 123, in _ds
return _do_segmentation(*args)
File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 205, in _do_segmentation
seg_out = core.call_quiet(
File "/usr/local/lib/python3.10/site-packages/cnvlib/core.py", line 32, in call_quiet
raise RuntimeError(
RuntimeError: Subprocess command failed:
$ Rscript --no-restore --no-environ /tmp/tmpula3kw8u
b'Loading probe coverages into a data frame\nWarning message:\nIn CNA(cbind(tbl$log2), tbl$chromosome, tbl$start, data.type = "logratio", :\n markers with missing chrom and/or maploc removed\n\nSegmenting the probe data\nError in segment(cna, weights = tbl$weight, alpha = 1e-04) : \n length of weights should be the same as the number of probes\nExecution halted\n'
This is the reason why no .cns
file is generated and the batch
command is terminated here.
I notice the weight column is empty in the .cnr
file:
$ head my_sample.cnr | column -t
chromosome start end gene depth log2 weight
chr1 150500 300849 Antitarget 0 -0.00216322
chr1 300849 451198 Antitarget 0 -0.00216322
chr1 451198 601547 Antitarget 0 -0.00216322
chr1 601547 751897 Antitarget 0 -0.00216322
chr1 751897 902246 Antitarget 0 -0.00216322
chr1 902246 1052595 Antitarget 0 -0.00216322
chr1 1052595 1202944 Antitarget 0 -0.00216322
chr1 1202944 1353294 Antitarget 0 -0.00216322
chr1 1353294 1503643 Antitarget 0 -0.00216322
Seems to be related to this issue.
Here is the quick fix.
cnvkit
output files are missing. There is no segmentation file.cns
and scatter and diagram plot files.pdf
in the output folder. They are not generated bycnvkit batch
module.