Getting Error in CorePanGenome.pl #2
Description
Hello, I am trying to run your script, however, the script is dying at line 100:
system($invoke_string); die if $?;
Not sure what's causing the script to die as I know I am passing the $checkpoint_passed since I am printing out CorePanGenome.pl: CorePanGenome::main: Running data/wyka/Fluidity/CorePanGenome_blaster.pl
So it's finding the correct $invoke_string
stephenwyka@bspmgenomics:/data/wyka/Fluidity$ ./CorePanGenome.pl Claviceps_purpurea_Clav04.gbk Claviceps_purpurea_Clav46.gbk Claviceps_purpurea_Clav55.gbk Claviceps_purpurea_LM207.gbk Claviceps_purpurea_LM232.gbk Claviceps_purpurea_LM28.gbk Claviceps_purpurea_LM30.gbk Claviceps_purpurea_LM469.gbk Claviceps_purpurea_LM474.gbk Claviceps_purpurea_LM4.gbk Claviceps_purpurea_LM582.gbk Claviceps_purpurea_LM71.gbk --min_ortho_coverage 0.74 --min_ortho_identity 0.74
CorePanGenome.pl: CorePanGenome::main: Temporary directory is /data/wyka/Fluidity/cptmp
CorePanGenome.pl: CorePanGenome::main: Running /data/wyka/Fluidity/CorePanGenome_blaster.pl /data/wyka/Fluidity/Claviceps_purpurea_Clav04.gbk /data/wyka/Fluidity/Claviceps_purpurea_Clav46.gbk /data/wyka/Fluidity/Claviceps_purpurea_Clav55.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM207.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM232.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM28.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM30.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM469.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM474.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM4.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM582.gbk /data/wyka/Fluidity/Claviceps_purpurea_LM71.gbk --min_ortho_coverage=0.74 --min_ortho_identity=0.74 --xcdir=/data/wyka/Fluidity/xcdir --tempdir=/data/wyka/Fluidity/cptmp --use_pbs=0 --pbs_queue=topaz_main --outfile_prefix=CorePanGenome.pl...
Died at ./CorePanGenome.pl line 100.