Re: Trouble installing HiC-Pro, HiC-Pro: command not found

[nservant]

Hi

According to your config, it seems that you have installed HiC-Pro in /data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0 (in PREFIX).

So then, you need to update your PATH variable or to call it using the full path ;  /data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/bin/HiC-pro

Best

On Thursday, 30 September 2021 at 00:10:15 UTC+2 ami...@uci.edu wrote:

Hello,

I am trying to install HiC-Pro on a slurm cluster but I am getting errors. I downloaded the Hi-C Pro repository to my system and created the HiC-Pro_v3.1.0 environment from the environment.yml file. I then ran the commands "make configure" and "make install". I updated the config-install.txt and config-hicpro.txt files, then tried to run HiC-Pro using this script:

#!/bin/bash

#SBATCH -A lab

#SBATCH -J hic_pro

#SBATCH -p standard

#SBATCH --nodes=1 ##number of nodes to use

#SBATCH --cpus-per-task=30 ##number of cores to use per node

#SBATCH -error=slurm-%J.err ##Error file

cd /dfs3b/mbt/aminaoh/hic-pro

HiC-Pro -i /dfs3b/mbt/aminaoh/Xenopus_HiC_Niu -o hic_test -c /dfs3b/mbt/aminaoh/HiC-Pro/config-hicpro.txt

However, I always get this error:

/export/spool/slurm/slurmd.spool/job8313018/slurm_script: line 11: HiC-Pro: command not found

This is what my config-install.txt looks like:

PREFIX = /data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0

BOWTIE2_PATH = /opt/rcic/Modules/modulefiles/BIOTOOLS/bowtie2/2.4.4

SAMTOOLS_PATH = /opt/rcic/Modules/modulefiles/BIOTOOLS/samtools/1.10

R_PATH = /opt/rcic/Modules/modulefiles/LANGUAGES/R/4.0.4

PYTHON_PATH = /opt/rcic/Modules/modulefiles/LANGUAGES/python/3.8.0

CLUSTER_SYS = SLURM

How can I fix this error?

Thank you,

Amina