cjfields/pbwa

Parallel bwa implementation

pbwa's Issues

[bwt_restore_bwt] fail to open file '/home/wangfeng/WorkSpace1/wangfeng/Data/ref/ref.fa.rbwt'. Abort!

[wangfeng@node1 WorkDir]$ /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA aln -f SaiPrefix \

/home/wangfeng/WorkSpace1/wangfeng/Data/ref/ref.fa
/home/wangfeng/WorkSpace1/wangfeng/Data/JPZ715/JPZ715_DHG04131_HJFFLCCXX_L2_1.clean.fq.gz
/home/wangfeng/WorkSpace1/wangfeng/Data/JPZ715/JPZ715_DHG04131_HJFFLCCXX_L2_2.clean.fq.gz
[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
Proc 0: [bwa_seq_open] seeked to 0 in /home/wangfeng/WorkSpace1/wangfeng/Data/JPZ715/JPZ715_DHG04131_HJFFLCCXX_L2_1.clean.fq.gz
Proc 0: [bwa_seq_open] seeked to 0 in /home/wangfeng/WorkSpace1/wangfeng/Data/JPZ715/JPZ715_DHG04131_HJFFLCCXX_L2_2.clean.fq.gz
Broadcasting BWT (this may take a while)... done!
Broadcasting BWT (this may take a while)... [bwt_restore_bwt] fail to open file '/home/wangfeng/WorkSpace1/wangfeng/Data/ref/ref.fa.rbwt'. Abort!
[node1:31843] *** Process received signal ***
[node1:31843] Signal: Aborted (6)
[node1:31843] Signal code: (-6)
[node1:31843] [ 0] /lib64/libpthread.so.0() [0x3bbde0f500]
[node1:31843] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bbda328a5]
[node1:31843] [ 2] /lib64/libc.so.6(abort+0x175) [0x3bbda34085]
[node1:31843] [ 3] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA() [0x404f86]
[node1:31843] [ 4] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA(bwt_restore_bwt+0x145) [0x407ca5]
[node1:31843] [ 5] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA(bwa_aln_core+0xb2) [0x408842]
[node1:31843] [ 6] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA(bwa_aln+0x19b) [0x408d9b]
[node1:31843] [ 7] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA(main+0x6c) [0x4279ec]
[node1:31843] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3bbda1ecdd]
[node1:31843] [ 9] /home/wangfeng/WorkSpace1/wangfeng/ProgramFiles/pBWA/pBWA() [0x404bd9]
[node1:31843] *** End of error message ***
Aborted (core dumped)
[wangfeng@node1 WorkDir]$

output .sam file written per process

Maybe use MPI/IO to write to one file? I can test this on two systems, our local SGI and a typical ROCKS cluster...

sampe paired-end estimation is done per-process, not for the entire *.sai set

See subject