Hi,
I'm using canu snapshot v2.2-development +82 changes (af771ef) on a linux system, and have issues with the bogart step of unitigging. This is using about 45x ONT reads on a 2.7gb mammal genome.
An assertion is failing in findPotentialOrphans, which is similar to the (idle) unresolved issue in #1831. Unfortunately I can't share the sequencing data at this time, as asked for in that issue. Using the ovl algorithm was proving to be extremely slow, so I tried using mhap even for trimming and tigging, which is not recommended in the docs, but was suggest by some colleagues in the USDA. I wasn't sure if that approximate algorithm could be the cause of the failed assertion, or if there is potentially some issue upstream.
I've included final lines in the unitigger.err file below.
==> MERGE ORPHANS.
computeErrorProfiles()-- Computing error profiles for 4946 tigs, with 32 threads.
computeErrorProfiles()-- Finished.
findPotentialOrphans()-- working on 4946 tigs.
findPotentialOrphans()-- found 4218 potential orphans.
mergeOrphans()-- flagged 146 bubble tigs with 8494 reads
mergeOrphans()-- placed 13 unique orphan tigs with 228 reads
mergeOrphans()-- shattered 2 repeat orphan tigs with 80 reads
mergeOrphans()-- ignored 34 tigs with 902 reads; failed to place
mergeOrphans()--
==> MARK SIMPLE BUBBLES.
using 0.010000 user-specified threshold
findPotentialOrphans()-- working on 4946 tigs.
read 845459 at 802795 743355 olap to read 1331274 hangs 61633 17804 -> coords 743355 741162
bogart: bogart/AS_BAT_MergeOrphans.C:229: void findPotentialOrphans(TigVector&, BubTargetList&, bool): Assertion `mincoord < maxcoord' failed.
Failed with 'Aborted'; backtrace (libbacktrace):
(null)::0 in (null)()
Thanks,
Alex
PS I think there is a typo in the .trimReads.log files in the 3-overlapbasedtrimming stage, it uses NOV for the message column where the header suggests NOC for no change. It appears here.
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