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Old 08-12-2021, 02:55 PM   #57
Sean Meaden
Junior Member
 
Location: New Zealand

Join Date: Aug 2021
Posts: 1
Default Core dump error with BBNorm

Hi all,
I'm using BBNorm to normalize a metagenomic dataset but am getting the following error during 'pass 1':

HTML Code:
Estimated unique kmers:         15483482031

Table creation time:            1619.850 seconds.
Started output threads.
/opt/nesi/CS400_centos7_bdw/BBMap/38.90-gimkl-2020a/bbnorm.sh: line 164: 106596 Bus error               (core dumped) java -ea -Xmx17653m -Xms17653m -cp /opt/nesi/CS400_centos7_bdw/BBMap/38.90-gimkl-2020a/current/ jgi.KmerNormalize bits=32 t=10 in=S1_all_R1_cpfy_clean.fq.gz in2=S1_all_R2_cpfy_clean.fq.gz out=S1_all_R1_cpfy_clean_norm.fq.gz out2=S1_all_R2_cpfy_clean_norm.fq.gz target=100 min=5
From manual I assumed that memory shouldn't be an issue, and have given 21G of memory to the job scheduler (slurm).

I'm wondering if I'm exceeding my storage with the temporary files that are created by BBNorm, although I should have ~10TB so wouldn't have thought that was the issue.

Any insight on this error would be much appreciated. Thanks in advance!
Sean
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