Hi,
Recently, I try to use samtools: Filter SAM or BAM, output SAM or BAM, but it reported that:
#############################
Set it manually or retry auto-detection
[E::hts_idx_push] Chromosome blocks not continuous
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I don't know what is wrong with it? Any help?
Thanks, Garen
Hello,
Did you try coordinate sorting the input BAM dataset first? That will probably resolve the problem, assuming that the BAM dataset is formatted correctly (header intact and reported alignments are present).
Support FAQs: https://galaxyproject.org/support/
If that does not work, and you can reproduce the problem at Galaxy Main, a bug report can be sent in. We are testing the pre-release of Galaxy 18.05 and would very much like to learn about new problems. Be sure to leave all inputs and the error dataset active (not deleted).
Thanks! Jen, Galaxy team
