I am running into a "Assertion `cnt > 0' failed" error in the assembly stage 4-unitigger. This is running on a cluster and so far this assembly ran without problems. I have restarted canu twice but the same error happens. We are using Canu 1.6 on a centos7 cluster with LSF job submission system.
This is from the unitigger.1.out:
Running job 1 based on LSB_JOBINDEX=1 and offset=0.
./unitigger.sh: line 75: 31378 Aborted (core dumped) $bin/bogart -G ../canu_assembly_subreads2.gkpStore -O ../canu_assembly_sub
reads2.ovlStore -o ./canu_assembly_subreads2 -gs 430000000 -eg 0.105 -eM 0.105 -mo 500 -dg 6 -db 6 -dr 3 -ca 2100 -cp 200 -threads 4 -M 20 -una
ssembled 2 0 1.0 0.5 5 > ./unitigger.err 2>&1
./unitigger.sh: line 87: ../canu_assembly_subreads2.ctgStore/seqDB.v001.sizes.txt: No such file or directory
Below is the error message from unitigger.err:
computeErrorProfiles()-- Computing error profiles for 141027 tigs, with 4 threads.
computeErrorProfiles()-- Finished.
placeContains()-- placing 970137 contained and 306780 unplaced reads, with 4 threads.
placeContains()-- Placed 656894 contained reads and 11575 unplaced reads.
placeContains()-- Failed to place 313243 contained reads (too high error suspected) and 295205 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 141027 reads in 1392714 tigs, with 4 threads.
optimizePositions()-- Allocating scratch space for 1392714 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 (null)()
bogart/AS_BAT_OptimizePositions.C::379 in ZN9TigVector17optimizePositionsEPKcS1()
bogart/bogart.C::456 in main()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()
I am running into a "Assertion `cnt > 0' failed" error in the assembly stage 4-unitigger. This is running on a cluster and so far this assembly ran without problems. I have restarted canu twice but the same error happens. We are using Canu 1.6 on a centos7 cluster with LSF job submission system.
This is from the unitigger.1.out:
Running job 1 based on LSB_JOBINDEX=1 and offset=0.
./unitigger.sh: line 75: 31378 Aborted (core dumped) $bin/bogart -G ../canu_assembly_subreads2.gkpStore -O ../canu_assembly_sub
reads2.ovlStore -o ./canu_assembly_subreads2 -gs 430000000 -eg 0.105 -eM 0.105 -mo 500 -dg 6 -db 6 -dr 3 -ca 2100 -cp 200 -threads 4 -M 20 -una
ssembled 2 0 1.0 0.5 5 > ./unitigger.err 2>&1
./unitigger.sh: line 87: ../canu_assembly_subreads2.ctgStore/seqDB.v001.sizes.txt: No such file or directory
Below is the error message from unitigger.err:
computeErrorProfiles()-- Computing error profiles for 141027 tigs, with 4 threads.
computeErrorProfiles()-- Finished.
placeContains()-- placing 970137 contained and 306780 unplaced reads, with 4 threads.
placeContains()-- Placed 656894 contained reads and 11575 unplaced reads.
placeContains()-- Failed to place 313243 contained reads (too high error suspected) and 295205 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 141027 reads in 1392714 tigs, with 4 threads.
optimizePositions()-- Allocating scratch space for 1392714 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 (null)()
bogart/AS_BAT_OptimizePositions.C::379 in ZN9TigVector17optimizePositionsEPKcS1()
bogart/bogart.C::456 in main()
(null)::0 in (null)()
(null)::0 in (null)()
(null)::0 in (null)()