cnvkit Error message "length of weights should be the same as the number of probes Execution halted"
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23 months ago
lhaiyan3 ▴ 60

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

sequencing cnvkit • 706 views
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Hey man... Do you have the solution for this issue? I'm asking because I'm having the exact same error!

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