Entering edit mode
4.3 years ago
lhaiyan3
▴
80
Hi, I am using the CNVkit 0.9.7.b1
for the wgs data.
I got the following wrong message:
RuntimeError: Subprocess command failed:
$ Rscript --vanilla /tmp/tmpg0ig1rdg
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-06) : \n length of weights should be the same as the number of probes\nExecution halted\n'
Here is my script,
cnvkit.py batch 7_JS0053CD062119.dd.bam \
-n 8_JS0053CD062319.dd.bam 9_JS0105CD081017.dd.bam \
-m wgs -f cnvkit_reference/hg19.fa \
--annotate cnvkit_reference/hg19_refFlat.txt
Can you please give me some suggestions?
Thanks, HY
Hey man... Do you have the solution for this issue? I'm asking because I'm having the exact same error!