April 1, 2016 at 10:43 pm #1857
Running this command:
$ novoalign -r Random -d D_rerio_RNA.nix -f run_1826_s_7_withindex_sequence.txt_TAATCATAA.fq > test.starve1.novout
generates this output:
Assertion failed: (tgt[tposn] != '\0'), function rptmismatch, file src/rptNative.cc, line 239. Abort trap: 6
It seems to sort of be working, as the output file includes several tags with the R in the 5th column.
I tried -r All, and that seems to work fine (at least, it didn’t die as quickly; I did not run it to completion).April 2, 2016 at 12:27 am #1858
What version of Novoalign are you using?April 4, 2016 at 1:49 am #1859
There is an issue in V3.04 where changes we made to support alternate scaffolds of GRC38 could result in a n invalid CIGAR for SAM format reports. The problem was caused by a failure to detail the correct alignment when using -r Random or -r All and could affect Native report format as well so as first step if you are using V3.04 could you upgrade to V3.04.04 which has a fix.April 4, 2016 at 4:51 pm #1860
I was running 3.04.01, upgraded, and it seems to be working fine.April 5, 2016 at 12:47 am #1861
That’s excellent. Thanks for the update.
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