Question: Facing problem in BWA reference genome mapping
0
gravatar for abdul.suboor123
3 months ago by
Huazhong Agricultural University, China
abdul.suboor1230 wrote:

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
bwa mapping genome • 196 views
ADD COMMENTlink written 3 months ago by abdul.suboor1230
2

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by ATpoint13k

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

ADD REPLYlink written 3 months ago by abdul.suboor1230
1

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

ADD REPLYlink written 3 months ago by ATpoint13k

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

ADD REPLYlink written 3 months ago by abdul.suboor1230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 691 users visited in the last hour