I am having a job crash in bogart on what I suspect is a memory error, but I don't know for sure
I've gone through many iterations of this, including these:
canu-1.7/Linux-amd64/bin/canu -assemble maxMemory=900g maxThreads=4 utgovlMemory=225g utgovlThreads=4 -d canu_data/tetra_canu -p tetra_canu genomeSize=1.3g batMemory=225g -pacbio-corrected canu_data/tetra_canu/trimmedReads.fasta.gz
canu-1.7/Linux-amd64/bin/canu -assemble maxMemory=300g maxThreads=16 utgovlMemory=200g utgovlThreads=8 -d canu_data/tetra_canu -p tetra_canu genomeSize=1.3g -pacbio-corrected canu_data/tetra_canu/trimmedReads.fasta.gz
All of the various parameter combinations I've tried result in the exact same output (other than differences from CLI parameters, e.g. thread number), even after removing the 4-unitigger/ dir.
I am running this on Amazon Linux.
I am attaching a unitigger.err file, which shows as much as I can tell about the error message here:
==> MERGE ORPHANS.
computeErrorProfiles()-- Computing error profiles for 145380 tigs, with 16 threads.
ERROR: stdDev is full; can't insert() new value.
This looks to me like some sort of allocation error, but I'm not enough of an expert to get much from going through the source code.
unitigger.log just has these lines, which I think might be a downstream phenomenon:
Running job 1 based on command line options.
./unitigger.sh: line 82: ../tetra_canu.ctgStore/seqDB.v001.sizes.txt: No such file or directory
../tetra_canu.ctgStore/ does not exist.
tetra_canu.005.mergeOrphans.thr004.num000.log, the only mergeOrphans log file in evidence, has a bunch of innocuous-looking lines:
WARNING: tig 19049 length 9064 nReads 393906 has 4873434470 overlaps.
WARNING: read 2955067 7992-0
WARNING: read 1498208 890-6341
WARNING: read 10125626 961-6908
WARNING: read 10277223 1039-7041
WARNING: read 7556593 7051-1064
WARNING: read 3855054 6880-1087
# etc.
I have increased available memory quite substantially (using ~1TB) and restarted the run multiple times with different thread/memory arguments but I think I'm misunderstanding something.
Do you have any suggestions?
Many thanks, max
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