I'm attempting to use your tool novoBreak by running 'run_novoBreak.sh', but it exits quite early on with the errors:
id2pair takes 14 seconds
begin sorting ids...
sorting ids takes 1 seconds
begin output results...
Outputting results takes 0 seconds
Finished
mkdir: cannot create directory `split': File exists
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
Can't exec "SSAKE": No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 34.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/run_ssake.pl line 39.
[gzclose] buffer error
No such file or directory at /bioinfo/guests/nriddifo/Modules/novobreak/infer_bp_v4.pl line 13.
Would you be able to provide some assistance? As far as I can see, there's no manual available, and it's hard for me to diagnose exactly what's causing the problem.
Thanks
Nick
Last edit: Nick Riddiford 2017-04-05
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
you should export the path to the novoBreak_distribution directory. The command should be "export PATH=$PATH:/data/tmp/huebnerj/novoBreak_distribution_v1.1.3rc".
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Zechen,
I'm attempting to use your tool novoBreak by running 'run_novoBreak.sh', but it exits quite early on with the errors:
I'm running as follows:
./bioinfo/novobreak/run_novoBreak.sh [novoBreak dir] [genome.fa] [tumour.bam] [normal.bam] 8 [out dir]Would you be able to provide some assistance? As far as I can see, there's no manual available, and it's hard for me to diagnose exactly what's causing the problem.
Thanks
Nick
Last edit: Nick Riddiford 2017-04-05
you should export the path to the novoBreak_distribution directory. The command should be "export PATH=$PATH:/data/tmp/huebnerj/novoBreak_distribution_v1.1.3rc".