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Old 03-03-2011, 02:33 PM   #1
libiyagirl
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Location: canada

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Posts: 27
Default can I automate running dindel?

Hello,

I am writing a script for automatically running dindel commands. But it never works.

For example, whenever I use:
"input_file=/path/input_file.bam
dindel --bamFile $input_file"

it can go to the path and find the file, but can not open or read it. I'm pretty sure the method is correct, because it works fine on samtools.

Any idea regarding this?

Thanks a lot,
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Old 03-03-2011, 02:45 PM   #2
Michael.James.Clark
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Might be the permissions of the file. Try:
Code:
chmod 755 /path/input_file.bam
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Old 03-03-2011, 03:11 PM   #3
libiyagirl
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Thank you Michael, it seems like chmod 755 can not change the permission of input.bam
Any solution?
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Old 03-03-2011, 04:42 PM   #4
Michael.James.Clark
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Try putting the input file path in quotes?

I.e.

Code:
input_file="/path/to/input_file.bam";
dindel --bamFile $input_file
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Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
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Old 03-04-2011, 06:19 AM   #5
mgogol
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Can you view the bam file?

samtools view input_file.bam | head

If you do ls -l on the bam file, what are the permissions that are shown?

What error message are you getting?
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Old 03-04-2011, 11:27 AM   #6
libiyagirl
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Thank you all, I used
input="$PATH/sorted.bam";
and it's working now!

Thanks a lot~!
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