I am trying to use bwa to perform alignment like the following:
#!/bin/sh
#PBS -S /bin/sh
#PBS -N run_aln
#PBS -m abe
#PBS -r n
#PBS -l walltime=100:00:00
#PBS -l mem=4GB
#PBS -l ncpus=1
#PBS -d /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1
#PBS -e localhost:/cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/errorfile_sam
#PBS -o localhost:/cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/outputfile_sam
/usr/local/bin/bwa sampe /cluster2/aimin/data_from_nature_publication/Reference/hg19 /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/1382_1_1.sai /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/1382_1_2.sai /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/1382_1_1.fastq /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/1382_1_2.fastq > /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/test_1382_1.sam
So far, I didn't get sam file yet, it already run more than 10 hours on our cluster. I don't know whether I did something wrong, or there are some problems on my command.
Does anyone can tell me how long it is takes for bwa to finish all alignment?
Thanks,
jlm
#!/bin/sh
#PBS -S /bin/sh
#PBS -N run_aln
#PBS -m abe
#PBS -r n
#PBS -l walltime=100:00:00
#PBS -l mem=4GB
#PBS -l ncpus=1
#PBS -d /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1
#PBS -e localhost:/cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/errorfile_sam
#PBS -o localhost:/cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/outputfile_sam
/usr/local/bin/bwa sampe /cluster2/aimin/data_from_nature_publication/Reference/hg19 /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/1382_1_1.sai /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/1382_1_2.sai /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/1382_1_1.fastq /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/1382_1_2.fastq > /cluster2/aimin/data_from_nature_publication/E-MTAB-197/E-MTAB-197.raw.3/test_1382_1/test_1382_1.sam
So far, I didn't get sam file yet, it already run more than 10 hours on our cluster. I don't know whether I did something wrong, or there are some problems on my command.
Does anyone can tell me how long it is takes for bwa to finish all alignment?
Thanks,
jlm