Hello! I'm having a difficult time figuring out why my MaSuRCA run keeps crashing. I've run it twice now and each run has lasted at least 5 days. The first time I qdel-ed the job myself due to a mismatch between the 'THREAD' and 'ppn'. The second time it crashed itself and I got no output file telling me what I did wrong.
The files that were generated include: combined_0, cutoff.txt, environment.sh, error_correct.log, meanAndStdevByPrefix.pe.txt, pa.renamed.fastq, pe.cor.fa, and pe_data.tmp.
I cross referenced these with this source (http://www.genome.umd.edu/docs/MaSuRCA_QuickStartGuide.pdf) to make sure that I wasn't missing anything, but I didn't find out anything useful. Can I learn anything about my run from these files? If not, what should my next step be?
Here are the contents of my config.txt file:
DATA PE = pa 500 75 /myPath/GSF1092-P1-ampc_S14_R1_001.fastq.gz /myPath/GSF1092-P1-ampc_S14_R2_001.fastq.gz END
PARAMETERS GRAPH_KMER_SIZE=auto USE_LINKING_MATES=1 NUM_THREADS=32 JF_SIZE=22500000000 DO_HOMOPOLYMER_TRIM=0
And my qsub:
PBS -N masurca_qsub
PBS -j oe
PBS -m abe
PBS -M email
PBS -q default
PBS -l nodes=1:ppn=32
workdir=myPath2 cd $workdir
Thanks in advance!