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Old 02-23-2015, 10:12 AM   #1
meenakshi
Junior Member
 
Location: Texas

Join Date: Feb 2015
Posts: 1
Question CREST extractSClip.pl Error

Hi All
I am getting the following error when I am trying to run "extractSClip.pl" from CREST package on a specific bam file. It runs fine on others! Here is the command and error:

command:
./extractSClip.pl -i /backup/cell-line/c727c60e-8ddd-1ddc-e040-ad451e414a77/G15511.HCC1143.2.bam -o /backup/cell-line/crest-out --ref_genome hg19.fa

Error:
substr outside of string at /usr/local/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm line 280.
Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/DB/Bam/AlignWrapper.pm line 280.



Any help is appreciated.

Thanks
M_A
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Old 04-08-2015, 02:09 AM   #2
chiara78
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Location: Uppsala, Sweden

Join Date: Apr 2015
Posts: 1
Default

Hi,

did you manage to solve this issue in the end? I'm getting the same error message today!

Thanks,

Chiara
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alignwrapper.pm, crest, extractsclip.pl

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