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Old 02-18-2013, 06:43 PM   #1
desse
Junior Member
 
Location: japan

Join Date: Sep 2012
Posts: 4
Default bwa 0.6.2 -sampe command does not work.

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.

Last edited by desse; 02-18-2013 at 06:44 PM. Reason: delete a icon
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