Facing problem in BWA reference genome mapping

Question

[abdul.suboor123]

I am trying for last four days and facing this issue, I am using PBS system, but when I submit the job and check with i.e. " sh bwa.pbs.e2343256 "after some steps it gets failed. check the commands below , and give me some suggestions about how to resolve this issue.

[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (176, 334, 769)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1955)
[M::mem_pestat] mean and std.dev: (448.13, 365.04)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2548)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
bwa: bwamem.c:1121: mem_reg2aln: Assertion `a.rid == ar->rid' failed.

bwa:532 terminated with signal 6 at PC=339c232925 SP=2af626684508.  Backtrace:
/lib64/libc.so.6(gsignal+0x35)[0x339c232925]
/lib64/libc.so.6(abort+0x175)[0x339c234105]
/lib64/libc.so.6[0x339c22ba4e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x339c22bb10]
bwa[0x43bb66]
bwa[0x43f243]
bwa[0x43c02f]
bwa[0x43e10a]
bwa[0x43c137]
bwa[0x4204a3]
/lib64/libpthread.so.0[0x339c6079d1]
/lib64/libc.so.6(clone+0x6d)[0x339c2e8b6d]

My PBS script is given below,

#!/bin/bash
#PBS -N bwa.pbs
#PBS -l nodes=1:ppn=8
#PBS -l walltime=2400:00:00
#PBS -q batch
#PBS -l mem=60G
#PBS -V

cd /public/home/skabdul/Data/circDNA/Mo17
bwa mem -T 19 Ref M1_PE400_R1.fq M1_PE400_R2.fq -O Output_file/M1.sam

[ATpoint]

Is -O really a capital O? If so:

-O INT[,INT]  gap open penalties for deletions and insertions [6,6]

You need a lowercase o, to redirect stdout to a file or simply bwa (...) > out.sam

The same goes for -T which should be -t to define thread number.

[abdul.suboor123]

yeah I have added -O capital, you mean if should be -o small?

[ATpoint]

Yes, both -t and -o must be small (lowercase). Please try the script again with these changes.

[abdul.suboor123]

Okay, Thank you so much... I am trying it again with these changes.