Guillaume Rizk
Guillaume Rizk
Hello, Yes I have been able to reproduce the error. It does not seem to come from your hashtable or from your binary. The problem seems to be in the...
Hello again, Forget what I said before, that would give you single-end mapping. The issue is because we do not support bam input sorted by coordinate, it should be sorted...
Hi, Thanks for your report. Although this is same error message as previous error reports in this thread, I am not sure this has a common cause. We are working...
@rpetrovski , from what I get, the picard tool compareSams does not care about output order and compares actual alignments. So problem may be deeper than that. Can --preserve-map-align-order true...
Hi, Our first assumption is that when not using `--preserve-map-align-order true` , then the insert sizes computation that is done at the beginning on first batch of reads may vary...
Hi, we have been able to reproduce the issue with your command line. The insert size statistics computed at the beginning does vary a little from one run to the...
Yes thanks, I got the files. I will check if there is some other issue.
Hi, Thank you for the suggestion, it indeed seems like a useful option when using uBAM files. We will look into it. Guillaume
Hi, and thanks for the update. Just to make sure, the crashes you experience are always in the hash building phase, not when doing mapping ?
Hi, Would you be able to share one of the random genome / command line that generates the problem ? Thanks, Guillaume