download issue for singularity image of HiC-Pro

[XuewenWangUGA]

The link to singularity .img is not supported, so the downloading has an issue. Error details:

This site can’t provide a secure connectionzerkalo.curie.fr uses an unsupported protocol. ERR_SSL_VERSION_OR_CIPHER_MISMATCH Unsupported protocol The client and server don't support a common SSL protocol version or cipher suite.

[wbszhu]

Hi, I have the same issue. this link is unsupported

[bakerwm]

Got the same error. The website URL is not valid: https://zerkalo.curie.fr/ @nservant Would you please help to check the URL, many thanks.

[bakerwm]

I have created a singularity image. But It is not working well on my test data, see bottom for the error message.

According to the documentation, I could build the Singularity image using the file Singularity, I can build the image on my local Ubuntu server, where I have the root account, So I can transfer the image file to HPC to work on my real data.

$ git clone https://github.com/nservant/HiC-Pro
$ cd HiC-Pro
$ sudo singularity build hicpro_latest.sif Singularity
$ singularity shell hicpro_latest.sif
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-binutils_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gcc_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gfortran_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gxx_linux-64.sh:10:40: parameter expansion requires a literal
Singularity> HiC-Pro -h
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

The test data could not be reached anyway. test_data, The website https://zerkalo.curie.fr reponse the error: ERR_SSL_VERSION_OR_CIPHER_MISMATCH

Errro on my test data:

$ apptainer run hicpro_latest.sif HiC-Pro -c config-hicpro.txt -i data/raw_data/ -o results
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-binutils_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gcc_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gfortran_linux-64.sh:10:40: parameter expansion requires a literal
source: /usr/local/conda/envs/hicpro/etc/conda/activate.d/activate-gxx_linux-64.sh:10:40: parameter expansion requires a literal

Run HiC-Pro 3.1.0
--------------------------------------------
Sun Jul 16 13:31:57 Asia 2023
Bowtie2 alignment step1 ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mapping_step1.log

--------------------------------------------
Sun Jul 16 13:33:24 Asia 2023
Bowtie2 alignment step2 ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mapping_step2.log

--------------------------------------------
Sun Jul 16 13:34:16 Asia 2023
Combine R1/R2 alignment files ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mapping_combine.log

--------------------------------------------
Sun Jul 16 13:34:17 Asia 2023
Mapping statistics for R1 and R2 tags ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mapping_stats.log

--------------------------------------------
Sun Jul 16 13:34:18 Asia 2023
Pairing of R1 and R2 tags ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mergeSAM.log

--------------------------------------------
Sun Jul 16 13:34:19 Asia 2023
Assign alignments to restriction fragments ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/mapped_2hic_fragments.log

--------------------------------------------
Sun Jul 16 13:36:30 Asia 2023
Merge chunks from the same sample ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/merge_valid_interactions.log

--------------------------------------------
Sun Jul 16 13:36:30 Asia 2023
Merge stat files per sample ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/merge_stats.log

--------------------------------------------
Sun Jul 16 13:36:30 Asia 2023
Run quality checks for all samples ...
Logs: logs/HiC_mHap_DMSO_2hr_rep1/make_Rplots.log
make: *** [/usr/local/bin/HiC-Pro_3.1.0/bin/../scripts//Makefile:181: hic_qc] Error 1

[bakerwm]

error fixed: The R library path was set to another directory in my config: ~/.Rprofile, which will overwrite the R library within the container. so return the above error Makefile:181: hic_qc.

comment on the following line in file ~/.Rprofile, and re-run the HiC-Pro command, everything goes well.

## file: ~/.Rprofile
# .libPaths("/data/yulab/wangming/Library/R/4.3/library")  ## User specific .libPath

In short：

$ git clone https://github.com/nservant/HiC-Pro
$ cd HiC-Pro
$ sudo singularity build hicpro_latest.sif Singularity
# modify the file config-hicpro.txt, update the following variables
# BOWTIE2_IDX_PATH, GENOME_SIZE, GENOME_FRAGMENT, PAIR1_EXT, PAIR2_EXT
$ singularity run hicpro_latest.sif HiC-Pro -i data -o results -c config-hicpro.txt