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Old 02-27-2013, 01:28 PM   #1
Lcontami
Junior Member
 
Location: France

Join Date: Feb 2013
Posts: 5
Default Bowtie2 'Could not open alignment output file' error

Hi,
here is my command line :
test is a directory that contains my index (genome.1.bt2 etc), and the two fastq files.

/usr/bin/bowtie2 -x genome -1 12344_TGACCA_L007_R1_001.fq -2 12344_TGACCA_L007_R2_001.fq -S /Documents/tests/test.sam

And the error message I get :

Error: Could not open alignment output file /Documents/tests/test.sam
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align --wrapper basic-0 -x genome -S /Documents/tests/test.sam -1 12344_TGACCA_L007_R1_001.fq -2 12344_TGACCA_L007_R2_001.fq

If you see what's wrong with my code please help me !
Thks
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Old 02-28-2013, 03:14 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,054
Default

Does your account have write permissions to the /Documents/tests directory?
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