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!
 https://www.biostars.org/u/24  




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.