HiC-Pro installation issue in FitHiChIP

[koushik20]

I have installed the HiC-Pro on my system. The below block confirms the installation of HiC-Pro

/home/koushik/Documents/FitHiChIP/HiC-Pro_3.1.0/bin/HiC-Pro -v
HiC-Pro version 3.1.0

I have added the above path to the .bashrc

export PATH="home/koushik/Documents/FitHiChIP/HiC-Pro_3.1.0/bin/:$PATH"

But when I run the FitHiChIP. I always get an error HiC-Pro is not installed in the system.

sudo bash FitHiChIP_Docker.sh -C configfile_BiasCorrection_CoverageBias_MCF7 

 ================ Verifying input configuration parameters =================
***** Specified output directory : ~/Documents/FitHiChIP/Hi-ChIP_demo
====>>> User did not provide any file in the COOL= option or the HIC= option or the Bed= option of the configuration file
==>>> So, the input interaction file is from the HiC-pro (valid pairs format)
==>>> But the matrix and bin interval files (HiC-pro) are not provided  - we need to generate them from HiC-pro
ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!

[koushik20]

I have exported the PATH in .bashrc and rebooted the system export PATH=$PATH:/home/koushik/Documents/FitHiChIP/HiC-Pro_3.1.0/bin

When I do echo $PATH I can see the updated path but still show the same error when running sudo bash FitHiChIP_Docker.sh -C configfile_BiasCorrection_CoverageBias_MCF10A

 ================ Verifying input configuration parameters =================
***** Specified output directory : ~/Documents/FitHiChIP/MCF10A-Rep_1
====>>> User did not provide any file in the COOL= option or the HIC= option or the Bed= option of the configuration file
==>>> So, the input interaction file is from the HiC-pro (valid pairs format)
==>>> But the matrix and bin interval files (HiC-pro) are not provided  - we need to generate them from HiC-pro
ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!

I have generated the .allValidPairs files using nf-core/hic. Is there a way to link the nextflow hic to FitHiChIP or would any suggestions be helpful?

Thank you!

[ay-lab]

Hi @koushik20 Please do not use FitHiChIP DOCKER or Singularity versions. They are outdated and need to be fixed to the current version. Please download the GitHub source code and install according to the documentation (https://ay-lab.github.io/FitHiChIP/html/index.html). It should solve the issues.

[koushik20]

I installed the FitHiChIP through the GitHub source code. The issue is with the HiC-Pro dependency in FitHiChIP. When I enter HiC-Pro -h I get an output.

usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v]
Use option -h|--help for more information

HiC-Pro 3.1.0
---------------
OPTIONS

   -i|--input INPUT : input data folder; Must contains a folder per sample with input files
   -o|--output OUTPUT : output folder
   -c|--conf CONFIG : configuration file for Hi-C processing
   [-p|--parallel] : if specified run HiC-Pro on a cluster
   [-s|--step ANALYSIS_STEP] : run only a subset of the HiC-Pro workflow; if not specified the complete workflow is run
      mapping: perform reads alignment - require fast files
      proc_hic: perform Hi-C filtering - require BAM files
      quality_checks: run Hi-C quality control plots
      merge_persample: merge multiple inputs and remove duplicates if specified - require .validPairs files
      build_contact_maps: Build raw inter/intrachromosomal contact maps - require .allValidPairs files
      ice_norm : run ICE normalization on contact maps - require .matrix files
   [-h|--help]: help
   [-v|--version]: version

I added the PATH of HiC-Pro to the .bashrc too but when I run sudo bash FitHiChIP_HiCPro.sh -C configfile_BiasCorrection_CoverageBias_MCF10A I always get HiC-Pro is not installed error.

 ================ Parsing input configuration file ================= 

Content of ValidPairs is /mnt/hicpro_results/allvalidpair_files/MCF10A_Rep1.allValidPairs
Content of Interval is 
Content of Matrix is 
Content of Bed is 
Content of HIC is 
Content of COOL is 
Content of ChrSizeFile is ./TestData/chrom_hg38.sizes
Content of PeakFile is /mnt/hichip_results/narrowpeak_files/MCF10A_H3k27ac.narrowPeak
Content of OutDir is ~/Documents/FitHiChIP/MCF10A-Rep_1
Content of CircularGenome is 0
Content of IntType is 3
Content of BINSIZE is 5000
Content of LowDistThr is 20000
Content of UppDistThr is 2000000
Content of UseP2PBackgrnd is 0
Content of BiasType is 1
Content of MergeInt is 1
Content of QVALUE is 0.01
Content of PREFIX is MCF10A_Rep-1
Content of OverWrite is 1

 ================ Verifying input configuration parameters ================= 

***** Specified output directory : ~/Documents/FitHiChIP/MCF10A-Rep_1
====>>> User did not provide any file in the COOL= option or the HIC= option or the Bed= option of the configuration file
==>>> So, the input interaction file is from the HiC-pro (valid pairs format)
==>>> But the matrix and bin interval files (HiC-pro) are not provided  - we need to generate them from HiC-pro
ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!

I followed these instructions to install HiC-Pro

[j-andrews7]

Hi @koushik20, did you solve this? I am running into the same problem.

[souryacs]

Hi @koushik20 and @j-andrews7 What is the output of the command "which HiC-Pro" in your systems? Please let me know.

[koushik20]

Which HiC-Pro /home/koushik/Documents/HiC-Pro_3.1.0/bin/HiC-Pro

The problem is that sudo is not recognizing the HiC-Pro and other dependencies paths so I added the /home/koushik/Documents/HiC-Pro_3.1.0/bin path into the secure path of sudo by sudo visudo command and FitHiChIP was successfully running.

[ay-lab]

Hi @koushik20 Thanks for your feedback. @j-andrews7, please let me know if the issue is resolved.