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Description
Hi, I got this error when using canu2.1 in hifi mode. I tried several times but can't fix it.
I also tried with canu2.0 and there was no error report.
I paste the log info here.
Waiting for your reply.
Best,
Dié TANG
-- Starting 'bat' concurrent execution on Fri Oct 9 15:36:23 2020 with 147465.78 GB free disk space (1 processes; 1 concurrently)
cd unitigging/4-unitigger
./unitigger.sh 1 > ./unitigger.000001.out 2>&1
-- Finished on Fri Oct 9 15:40:47 2020 (264 seconds) with 147465.736 GB free disk space
----------------------------------------
--
-- Bogart failed, retry
--
--
-- Running jobs. Second attempt out of 2.
----------------------------------------
-- Starting 'bat' concurrent execution on Fri Oct 9 15:40:47 2020 with 147465.736 GB free disk space (1 processes; 1 concurrently)
cd unitigging/4-unitigger
./unitigger.sh 1 > ./unitigger.000001.out 2>&1
-- Finished on Fri Oct 9 15:45:08 2020 (261 seconds) with 147465.637 GB free disk space
----------------------------------------
--
-- Bogart failed, tried 2 times, giving up.
--
ABORT: canu 2.1
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting. If that doesn't work, ask for help.
ABORT:
ABORT: Disk space available: 147465.637 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (unitigging/4-unitigger/unitigger.err):
ABORT:
ABORT: mergeOrphans()-- ignored 3 tigs with 17 reads; failed to place
ABORT: mergeOrphans()--
ABORT:
ABORT: ==> MARK SIMPLE BUBBLES.
ABORT: using 0.010000 user-specified threshold
ABORT:
ABORT:
ABORT: findPotentialOrphans()-- working on 1826 tigs.
ABORT: findPotentialOrphans()-- found 1385 potential orphans.
ABORT: mergeOrphans()-- flagged 1312 bubble tigs with 193436 reads
ABORT: mergeOrphans()-- placed 0 unique orphan tigs with 0 reads
ABORT: mergeOrphans()-- shattered 0 repeat orphan tigs with 0 reads
ABORT: mergeOrphans()-- ignored 2 tigs with 26 reads; failed to place
ABORT: mergeOrphans()--
ABORT: classifyAsUnassembled()-- 0 tigs 0 bases -- singleton
ABORT: classifyAsUnassembled()-- 0 tigs 0 bases -- too few reads (< 2 reads)
ABORT: classifyAsUnassembled()-- 0 tigs 0 bases -- too short (< 0 bp)
ABORT: classifyAsUnassembled()-- 0 tigs 0 bases -- single spanning read (> 1.000000 tig length)
ABORT: classifyAsUnassembled()-- 16 tigs 337525 bases -- low coverage (> 0.500000 tig length at < 3 coverage)
ABORT: classifyAsUnassembled()-- 1657 tigs 846330607 bases -- acceptable contigs
ABORT:
ABORT:
ABORT: ==> GENERATING ASSEMBLY GRAPH.
ABORT:
ABORT: computeErrorProfiles()-- Computing error profiles for 1826 tigs, with 16 threads.
ABORT: computeErrorProfiles()-- Finished.
ABORT:
ABORT: AssemblyGraph()-- allocating vectors for placements, 48.930MB
ABORT: AssemblyGraph()-- finding edges for 996744 reads (766997 contained), ignoring 72158 unplaced reads, with 16 threads.
ABORT: AssemblyGraph()-- building reverse edges.
ABORT: AssemblyGraph()-- build complete.
ABORT:
ABORT: ==> BREAK REPEATS.
ABORT:
ABORT: computeErrorProfiles()-- Computing error profiles for 1826 tigs, with 16 threads.
ABORT: computeErrorProfiles()-- Finished.
ABORT: bogart: bogart/AS_BAT_MarkRepeatReads.C:887: std::vector<breakReadEnd> buildBreakPoints(TigVector&, Unitig*, intervalList<int>&, intervalList<int>&, std::vector<confusedEdge>&): Assertion `isRepeat == true' failed.
ABORT:
ABORT: Failed with 'Aborted'; backtrace (libbacktrace):
ABORT: utility/src/utility/system-stackTrace.C::83 in _Z17AS_UTL_catchCrashiP7siginfoPv()
ABORT: (null)::0 in (null)()
ABORT: (null)::0 in (null)()
ABORT: (null)::0 in (null)()
ABORT: (null)::0 in (null)()
ABORT: (null)::0 in (null)()
ABORT: bogart/AS_BAT_MarkRepeatReads.C::887 in _Z16buildBreakPointsR9TigVectorP6UnitigR12intervalListIiES5_RSt6vectorI12confusedEdgeSaIS7_EE()
ABORT: bogart/AS_BAT_MarkRepeatReads.C::1051 in _Z15markRepeatReadsP13AssemblyGraphR9TigVectordjdRSt6vectorI12confusedEdgeSaIS4_EE()
ABORT: bogart/bogart.C::656 in main()
ABORT: (null)::0 in (null)()
ABORT: (null)::0 in (null)()
ABORT:
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