Hi,
I use bwa to align sequence data (Paired End Data from Ilumina).
I used bwa 0.6.2 but get stucked.
Here is what I have done so far:
Index:
bwa index -a is allchr.fa
(I got
.amb
.ann
.bwt
.fai
.pac
.sa)
Alignment: pc_n.sh program
REFERENCE=/Users/referenceData/chrall.fa
$BWA aln -t 8 $REFERENCE $QUERY1 > $3_1.sai
$BWA aln -t 8 $REFERENCE $QUERY2 > $3_2.sai
$BWA sampe $REFERENCE $3_1.sai $3_2.sai $QUERY1 $QUERY2 > $3_out.sam
And here is my Problem(message on terminal):
[main] Version: 0.6.2-r126
[main] CMD: /usr/bin/bwa sampe /Users/referenceData/chrall.fa mi_1.sai mi_2.sai q1.fq q2.fq
[main] Real time: 43.905 sec; CPU: 42.962 sec
/Users/pc_n.sh: line 44: mi_out.sam: command not found
/Users/pc_n.sh: line 44 is "$BWA sampe $REFERENCE $3_1.sai $3_2.sai $QUERY1 $QUERY2 > $3_out.sam"
This program worked using 0.5.9 version in the other PC.
Please help me.
I use bwa to align sequence data (Paired End Data from Ilumina).
I used bwa 0.6.2 but get stucked.
Here is what I have done so far:
Index:
bwa index -a is allchr.fa
(I got
.amb
.ann
.bwt
.fai
.pac
.sa)
Alignment: pc_n.sh program
REFERENCE=/Users/referenceData/chrall.fa
$BWA aln -t 8 $REFERENCE $QUERY1 > $3_1.sai
$BWA aln -t 8 $REFERENCE $QUERY2 > $3_2.sai
$BWA sampe $REFERENCE $3_1.sai $3_2.sai $QUERY1 $QUERY2 > $3_out.sam
And here is my Problem(message on terminal):
[main] Version: 0.6.2-r126
[main] CMD: /usr/bin/bwa sampe /Users/referenceData/chrall.fa mi_1.sai mi_2.sai q1.fq q2.fq
[main] Real time: 43.905 sec; CPU: 42.962 sec
/Users/pc_n.sh: line 44: mi_out.sam: command not found
/Users/pc_n.sh: line 44 is "$BWA sampe $REFERENCE $3_1.sai $3_2.sai $QUERY1 $QUERY2 > $3_out.sam"
This program worked using 0.5.9 version in the other PC.
Please help me.