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Starting on : Fri Mar 26 17:10:20 EDT 2021
Running on node : scc-pi2
Current directory : /projectnb2/ysapp/examples/newEx/bwa/qsub
Current job ID : 5535181
Current job name : bwa_example
Number of cores: 2
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/var/spool/sge/scc-pi2/job_scripts/5535181: line 47: [!-e: command not found
../ref/example_ref index already exists!
bwa aln -I -t 2 ../ref/example_ref ../data/reads.fq > ../out/bwa_example_aln.sai
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.00 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.17-r1188
[main] CMD: bwa aln -I -t 2 ../ref/example_ref ../data/reads.fq
[main] Real time: 0.004 sec; CPU: 0.004 sec
bwa samse ../ref/example_ref ../out/bwa_example_aln.sai ../data/reads.fq > ../out/bwa_example_aln.sam
[bwa_aln_core] convert to sequence coordinate... 0.00 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 250 sequences have been processed.
[main] Version: 0.7.17-r1188
[main] CMD: bwa samse ../ref/example_ref ../out/bwa_example_aln.sai ../data/reads.fq
[main] Real time: 0.005 sec; CPU: 0.002 sec
DONE!