nmb85
commented
8 years ago "Can I run it with qsub instead of bsub?" FWIW, I've been running my jobs with qsub without any problems. This PDF gives you a one-for-one conversion between the qsub (SGE) and bsub (LSF) options. Maybe later this weekend I'll post a modified create_jobs.py for SGE.
Here is an example of an LSF script modified for SGE. the header, PATH, and SGE_TASK_ID need to be changed:
#!/bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -N KmerCorpus
#$ -t 1-6:1
#$ -o ./Logs/KmerCorpus.out
#$ -e ./Logs/KmerCorpus.err
#$ -q micro
PATH=...
export PATH
echo Date: `date`
t1=`date +%s`
sleep $(($SGE_TASK_ID % 60))
python LSA/kmer_corpus.py -r ${SGE_TASK_ID} -i ./hashed_reads/ -o ./cluster_vectors/
[ $? -eq 0 ] || echo 'JOB FAILURE: $?'
echo Date: `date`
t2=`date +%s`
tdiff=`echo 'scale=3;('$t2'-'$t1')/3600' | bc`
echo 'Total time: '$tdiff' hours'
brian-cleary
hello！ I ran the LSA with the test data, and had some problem. I don't know how to solve. The first and second steps succeed, but the third step "bash ReadPartitioning.sh 4" with the problem:
Fri Oct 30 01:57:27 CST 2015 partitioning reads in hashed input file 4 printing end of last log file... Traceback (most recent call last): File "LSA/write_partition_parts.py", line 71, in
G = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0,2hashobject.hash_size,2hashobject.hash_size/5
0)]
ValueError: range() step argument must not be zeroG = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0
,2hashobject.hash_size,2hashobject.hash_size/50)]
0)] ValueErrorValueError: : range() step argument must not be zerorange() step argument must not be zeroG = [open('%s%s.%s.cols.%d' % (tmpdir,sample_id,outpart,i),'w') for i in range(0,2hashobject.hash_size,2hashobject.hash_size/50)]
And my datasets are more than 30Gb. Can I run it with qsub instead of bsub?
Thanks!