Hello everyone,
I am new at CNVKit. I installed it using conda and installed DNAcopy library to R but when I run cnvkit.py batch, I have this error:
`
Traceback (most recent call last):
File "/home/huk/anaconda3/envs/cnvkit/bin/cnvkit.py", line 8, in
sys.exit(main())
^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/commands.py", line 194, in _cmd_batch
pool.submit(
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/parallel.py", line 18, in submit
return SerialFuture(func(args))
^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/batch.py", line 264, in batch_run_sample
segments = segmentation.do_segmentation(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 79, in do_segmentation
rets = list(
^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 123, in _ds
return _do_segmentation(args)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 205, in _do_segmentation
seg_out = core.call_quiet(
^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/core.py", line 32, in call_quiet
raise RuntimeError(
RuntimeError: Subprocess command failed:
$ Rscript --no-restore --no-environ /tmp/tmpwesj11ie
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'
`
I am using a flatReferece created using "reference" command since I do not have any control samples. My data is a sequencing result of multiple exons of a single gene.
etal
commented
2 months ago
Hello everyone, I am new at CNVKit. I installed it using conda and installed DNAcopy library to R but when I run cnvkit.py batch, I have this error:
` Traceback (most recent call last): File "/home/huk/anaconda3/envs/cnvkit/bin/cnvkit.py", line 8, in
sys.exit(main())
^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/commands.py", line 194, in _cmd_batch
pool.submit(
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/parallel.py", line 18, in submit
return SerialFuture(func(args))
^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/batch.py", line 264, in batch_run_sample
segments = segmentation.do_segmentation(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 79, in do_segmentation
rets = list(
^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 123, in _ds
return _do_segmentation(args)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/segmentation/init.py", line 205, in _do_segmentation
seg_out = core.call_quiet(
^^^^^^^^^^^^^^^^
File "/home/huk/anaconda3/envs/cnvkit/lib/python3.11/site-packages/cnvlib/core.py", line 32, in call_quiet
raise RuntimeError(
RuntimeError: Subprocess command failed:
$ Rscript --no-restore --no-environ /tmp/tmpwesj11ie
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' `
My code is:
cnvkit.py batch cnvtest.bam -n -t test.bed -f hg19_v0_Homo_sapiens_assembly19.fasta --output-reference /home/huk/Desktop/Tool/cnvkit_test/FlatReference.cnn -d cnvtest/I am using a flatReferece created using "reference" command since I do not have any control samples. My data is a sequencing result of multiple exons of a single gene.
Thank you in advance.