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Question: (Closed) Samtool cant read .bed file
0
gravatar for GPS
4.5 years ago by
GPS • 20
India
GPS • 20 wrote:

hello

i am using SoftSearch tool that tool execute by command prompt and result will display in .vcf file 

but when I execite this by command 

 perl ./SoftSearch.pl -b Small_test.bam -f chr1.small.fa 

it will show one error "samtools: Could not read file "patxwhcm.bed": No such file or director"

can any one please tell me solution on this.

 

Thank You

 
samtools • 1.1k views
ADD COMMENT • link •
written 4.5 years ago by GPS • 20

Hello GPS!

Question is answered and follow-up is in other posts.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

Cheers!

ADD REPLY • link modified 4.5 years ago • written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi GPS,

we do not know about your SoftSearch Tool, and in your question is no code. It is also not Galaxy releated. Please try to debug the softsearch.pl script. My guess is that you generated patxxxx.bed file is not available, or the specified the wrong path to samtools.

Cheers,

Bjoern
ADD COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

Thanks for the reply to me.

This is link from I install the softsearch tool 

https://code.google.com/p/softsearch/ 

Thank You

GPS

 

ADD REPLY • link written 4.5 years ago by GPS • 20

Hi,

I never used Softsearch so I can't help much with it. For me it seems to be a Softsearch issue and not a Galaxy one.

Is the program running in your terminal? Does the tools do something wired with file handling, like changing working directories or so?

 

ADD REPLY • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k
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