Question: cnvkit bgzf_read error 4 after 4 bytes
1
gravatar for sm.hashemin
11 months ago by
sm.hashemin90
sm.hashemin90 wrote:

Hi, I am running CNVKIT and I am new to it. I was running a batch on two tumor samples with a flat reference.

anaconda3/bin/cnvkit.py batch 1.bam 2.bam -n -t /refseq_exome_genesymbol_headless_CNVkit.csv -f hg19.fasta --access access-5k-mappable.hg19.bed --output-reference my_flat_reference.cnn -d output -p 6

I get

 [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes

but it still continues to run. Is it because my bam files are not bzipped? could the results still be usable?

Thanks a lot in advance! Eric T.

bzip samtools cnvkit • 432 views
ADD COMMENTlink modified 11 months ago by Eric T.2.6k • written 11 months ago by sm.hashemin90
1

what is the output of

file 1.bam 2.bam

should be something like "bam version 1" or " gzip compressed data, extra field"

ADD REPLYlink written 11 months ago by Pierre Lindenbaum129k

thanks for you answer. It says gzip compressed data, extra field

ADD REPLYlink written 11 months ago by sm.hashemin90
2
gravatar for Eric T.
11 months ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

That's odd. CNVkit reads the input BAM files with pysam, which internally uses htslib, the same as samtools. If samtools can read (e.g. index) your BAM files, then they should work fine with CNVkit. I haven't seen that error/warning myself, but if the process continues to run and the outputs from the CNVkit command look reasonable then maybe it's not a problem.

ADD COMMENTlink written 11 months ago by Eric T.2.6k
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