issue on CRAM: can't resolve www.ebi.ac.uk:80: System error

[dolittle007]

sambamba version 0.6.8

sambamba view -T $HOME/database/genome/hg38.fa -f cram test.bam -o test.cram

It pop ups a warning message: can't resolve www.ebi.ac.uk:80: System error. How to suppress it?

[milankovacevicsbg]

sambamba version 0.7.0

CMD: sambamba-0.7.0 view --cram-input --nthreads=8 --format=bam merged-normal.filtered.cram -o merged-normal.filtered.bam

ERROR: can't resolve www.ebi.ac.uk:80: System error Failed to populate reference for id 20 Slice ends beyond reference end. Unable to fetch reference #20 11038960..14992653 can't resolve www.ebi.ac.uk:80: System error Failed to populate reference for id 20 Slice ends beyond reference end. Unable to fetch reference #20 16339775..18977207 can't resolve www.ebi.ac.uk:80: System error Failed to populate reference for id 20 Slice ends beyond reference end. Unable to fetch reference #20 15599451..16339850 can't resolve www.ebi.ac.uk:80: System error Failed to populate reference for id 20 Slice ends beyond reference end.

After which tool just fails. Any idea why? Thanks!

[pjotrp]

Sambamba uses an older htslib for CRAM which has

    htslib/cram/cram_io.c:  ref_path = "http://www.ebi.ac.uk:80/ena/cram/md5/%s";

I recommend against using sambamba for CRAM. We'll rip the support out most likely.

[milankovacevicsbg]

Thanks, Pjotr!