Bwa on multiple processor

Hi Guys,

When I am trying to run bwa mem on multiple processor, I am getting error as :

> mpirun -np 16 bwa mem hg19-agilent.fasta R1.fastq  R2.fastq  | samtools sort  -o aln.bam

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 81550 sequences (10000056 bp)...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 81550 sequences (10000056 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81100 sequences (10000119 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::process] read 81550 sequences (10000056 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 30319, 18, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (143, 297, 517)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1265)
[M::mem_pestat] mean and std.dev: (327.33, 289.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1639)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 126, 162)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 290)
[M::mem_pestat] mean and std.dev: (132.56, 47.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 354)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (50, 128, 341)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 923)
[M::mem_pestat] mean and std.dev: (184.25, 219.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1214)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 176, 1975)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5629)
[M::mem_pestat] mean and std.dev: (759.27, 1220.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7456)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 30319, 18, 12)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (143, 297, 517)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1265)
[M::mem_pestat] mean and std.dev: (327.33, 289.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1639)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (98, 126, 162)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 290)
[M::mem_pestat] mean and std.dev: (132.56, 47.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 354)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (50, 128, 341)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 923)
[M::mem_pestat] mean and std.dev: (184.25, 219.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1214)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (148, 176, 1975)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5629)
[M::mem_pestat] mean and std.dev: (759.27, 1220.33)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 7456)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 81100 reads in 31.031 CPU sec, 30.964 real sec
[M::mem_process_seqs] Processed 81100 reads in 31.117 CPU sec, 31.004 real sec
[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] Parse error at line 27849
samtools sort: truncated file. Aborting

It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT — mpirun was only
notified of the first one, which was on node n0).

mpirun can only be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the “lamexec” program
to run non-MPI programs over the lambooted nodes.

While when I am running it as below, it gets completed successfully.

bwa mem hg19-agilent.fasta R1.fastq R2.fastq | samtools sort -o aln.bam

Is there any issue running with multiple processor?
Please suggest.

Thanks and regards

Read more here: Source link