can I automate running dindel?

libiyagirl · 03-03-2011, 03:33 PM

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,

Michael.James.Clark · 03-03-2011, 03:45 PM

Might be the permissions of the file. Try:

Code:

chmod 755 /path/input_file.bam

libiyagirl · 03-03-2011, 04:11 PM

Thank you Michael, it seems like chmod 755 can not change the permission of input.bam
Any solution?

Michael.James.Clark · 03-03-2011, 05:42 PM

Try putting the input file path in quotes?

I.e.

Code:

input_file="/path/to/input_file.bam";
dindel --bamFile $input_file

mgogol · 03-04-2011, 07:19 AM

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?

libiyagirl · 03-04-2011, 12:27 PM

Thank you all, I used
input="$PATH/sorted.bam";
and it's working now!

Thanks a lot~!

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03-03-2011, 03:33 PM	#1
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	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,

03-03-2011, 03:45 PM	#2
Michael.James.Clark Senior Member Location: Palo Alto Join Date: Apr 2009 Posts: 213	Might be the permissions of the file. Try: Code: chmod 755 /path/input_file.bam __________________ Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] *Projects*: U87MG whole genome sequence [Website] [Paper]

03-03-2011, 05:42 PM	#4
Michael.James.Clark Senior Member Location: Palo Alto Join Date: Apr 2009 Posts: 213	Try putting the input file path in quotes? I.e. Code: input_file="/path/to/input_file.bam"; dindel --bamFile $input_file __________________ Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] *Projects*: U87MG whole genome sequence [Website] [Paper]

03-03-2011, 04:11 PM	#3
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Thank you Michael, it seems like chmod 755 can not change the permission of input.bam Any solution?

03-04-2011, 07:19 AM	#5
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	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?

03-04-2011, 12:27 PM	#6
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Thank you all, I used input="$PATH/sorted.bam"; and it's working now! Thanks a lot~!