I just started using CAFTOOLS and I am currently trying to run phrap2gap on a test group of 10 EXP files.
The process fails continously (no matter which options i choose) with the error
Bad file descriptor
I guess what I am looking for is an example (other than those on the CAF website or in the paper "sequnce Assemply with CAFTOOLS" to steer me down the right path. Can anyone help me with this.
alternatively if i simply run caf_phrap on my caf db after some processing i get the following error
Aligning reads to contigs ...sh: line 1: 11008 Segmentation fault phrap ./Phrap/CAF -old_ace -forcelevel 0 >./Phrap/CAF.stdout
Failed: phrap ./Phrap/CAF -old_ace -forcelevel 0 > ./Phrap/CAF.stdout: No such file or directory