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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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Cannot open bamfile `sample.clean.bam` (sam: reference already used) #1

Closed DieTANG closed 6 years ago

DieTANG commented 6 years ago

I was using ALLHiC to deal with a haploid genome. Thus I skip the prune step, but when I run the ALLHiC_partition cmd, I got this error.

tangerzhang commented 6 years ago

Could you please post the command lines that you used to generate the bam files? Also, please indicate the version of samtools you are using. We've tested ALLHiC only on samtools v1.9. Higher version should be OK. But using version 1.3 should be problematic.

DieTANG commented 6 years ago

Yes, it's the samtools version problem. Thanks!