CREST extractSClip.pl Error

[meenakshi]

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

[chiara78]

Hi,

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

Thanks,

Chiara