bogart failed

[tangerzhang]

Please see below for the bogart error message. I've swith -M 20 to -M 200 to increase the memory in bogart command, but still can not pass this step.

###Command line:
canu -s spec.txt -p Ever -d Asm genomeSize=400m -pacbio-raw Ever/*.fastq gnuplotTest=true

###spec.txt
gridOptions="-N canu -l walltime=30000:00:00 -q high"
corOutCoverage=150
ovbMemory=8g
maxMemory=500g
maxThreads=48
ovsMemory=8-500g
ovsThreads=4
oeaMemory=32g
ovsMethod=parallel

###canu --version
Canu 1.6

###system
SGE Gird

###Error message
optimizePositions()-- Reset zero.
optimizePositions()-- Checking convergence.
optimizePositions()-- converged: 4419693 reads
optimizePositions()-- changed: 1545 reads
optimizePositions()-- Expanding short reads with 4 threads.
optimizePositions()-- Updating positions.
optimizePositions()-- Finished.

==> PLACE CONTAINED READS.

computeErrorProfiles()-- Computing error profiles for 27235 tigs, with 4 threads.
computeErrorProfiles()-- Finished.

placeContains()-- placing 4264496 contained and 68921 unplaced reads, with 4 threads.
placeContains()-- Placed 3987634 contained reads and 4437 unplaced reads.
placeContains()-- Failed to place 276862 contained reads (too high error suspected) and 64484 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 27235 reads in 4421238 tigs, with 4 threads.
optimizePositions()-- Allocating scratch space for 4421238 reads (0 KB).
optimizePositions()-- Initializing positions with 4 threads.
bogart: bogart/AS_BAT_OptimizePositions.C:140: void Unitig::optimize_initPlace(uint32, optPos*, optPos*, bool, std::set&, bool): Assertion `cnt > 0' failed.

Failed with 'Aborted'; backtrace (libbacktrace):
AS_UTL/AS_UTL_stackTrace.C::102 in _Z17AS_UTL_catchCrashiP9siginfo_tPv()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
bogart/AS_BAT_OptimizePositions.C::140 in _ZN6Unitig18optimize_initPlaceEjP6optPosS1_bRSt3setIjSt4lessIjESaIjEEb()
bogart/AS_BAT_OptimizePositions.C::391 in ZN9TigVector17optimizePositionsEPKcS1._omp_fn.0()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()

[skoren]

This was a bug in earlier versions (see #873, #874, #844). You can try the patches in issue #873 to see if it fixes your crash. Otherwise, same options as in that case apply, the easiest would be to re-run the unitigging step using the trimmed reads with the latest code.