Closed bozbezbozzel closed 1 year ago
will try this suggestion: https://github.com/etal/cnvkit/issues/678 and update
My reference genome uses 1, 2, 3 etc...
for the chromosomes and so do my sample bams:
less Homo_sapiens.GRCh38.dna.primary_assembly.fa | grep ">"
>1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
>10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF
>11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF
@HD VN:1.6 GO:none SO:coordinate
@SQ SN:1 LN:248956422 M5:2648ae1bacce4ec4b6cf337dcae37816
@SQ SN:10 LN:133797422 M5:907112d17fcb73bcab1ed1c72b97ce68
@SQ SN:11 LN:135086622 M5:1511375dc2dd1b633af8cf439ae90cec
I used the exact same reference genome file for every step and I'm coming from unmapped BAMs.
Solved-- had to remove contigs from my antitarget and target input files.
got the same error, and my reference genome uses chr1, chr2..would you suggest I replace all with 1, 2, 3, and try again?
CNVkit is able to read the .bed file with targets that I give it, it makes a target.bed, it processes my normal samples which appears to go well. Then I get the following error:
followed by "Errors in BED line" for every single line in the file, followed by
with again every.single.line.
I can run
samtools bedcov
just fine on my original bed file. CNVkit can read, process, and write out this target bed. So what's throwing me for a loop is that CNVkit cannot adequately process the file it wrote out itself.What I've done:
cat -t
I'm out of ideas. I have no idea what's causing this-- surely if my original bed had something wrong with it, CNVkit would fail on the first step of trying to write out the target.bed file?
I'm running CNVkit 0.9.9 in python 3.9 with
snakemake 7.8.5
.pysam 0.19.1
andsamtools 1.10
.