Closed dolittle007 closed 4 years ago
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!
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.
Thanks, Pjotr!
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?