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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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/scripts//hic.inc.sh: No such file or directory #312

Closed harbourlab closed 4 years ago

harbourlab commented 4 years ago

Has anyone encountered this when trying to run? Would appreciate any help!

harbourlab commented 4 years ago

(Stefan_HiChIP) [sxk321@pegasus Stefan_Hi_ChIP]$ HiC-Pro -i Data -o HiC_output -c config-hicpro.txt /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 134: /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/../scripts//hic.inc.sh: No such file or directory /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 136: abspath: command not found /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 137: abspath: command not found /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 145: die: command not found /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 148: abspath: command not found /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 153: abspath: command not found /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/HiC-Pro: line 246: die: command not found mkdir: missing operand Try mkdir --help' for more information. ln: creating symbolic link./': File exists cp: cannot create regular file `/config-hicpro.txt': Permission denied

Run HiC-Pro 2.10.0 make: /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/../scripts//Makefile: No such file or directory make: No rule to make target `/nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/../scripts//Makefile'. Stop. make: /nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/../scripts//Makefile: No such file or directory make: No rule to make target `/nethome/sxk321/miniconda3/envs/Stefan_HiChIP/bin/../scripts//Makefile'. Stop.

harbourlab commented 4 years ago

Solved.. HiC-Pro needs to be run with the full path to work.