Error in Hi-C Pro non processing all the files

[robertferr]

I run the second script for Hi-C Pro after the bowtie2 alignment and the script seems to have problem processing all the files (in the "Merge chunks from the same sample" and "Generate binned matrix files") then stopping at the sample 3 and not proceeding with the script for the "qc part". This is the error:

---

Sat Nov 9 09:41:59 CET 2024
Merge chunks from the same sample ...
Logs: logs/sample1/merge_valid_interactions.log
Logs: logs/sample2/merge_valid_interactions.log
Logs: logs/sample3/merge_valid_interactions.log

---

Sat Nov 9 09:58:30 CET 2024
Merge stat files per sample ...
Logs: logs/sample1/merge_stats.log
Logs: logs/sample2/merge_stats.log
Logs: logs/sample3/merge_stats.log
Logs: logs/sample4/merge_stats.log
Logs: logs/sample5/merge_stats.log
Logs: logs/sample6/merge_stats.log

---

Sat Nov 9 09:58:32 CET 2024
Generate binned matrix files ...
Logs: logs/sample1/build_raw_maps.log
Logs: logs/sample2/build_raw_maps.log
Logs: logs/sample3/build_raw_maps.log

---

Sat Nov 9 10:17:11 CET 2024
Run quality checks for all samples ...
Logs: logs/sample1/make_Rplots.log
Logs: logs/sample2/make_Rplots.log
Logs: logs/sample3/make_Rplots.log
make: *** [/hpc/home/roberto.ferrari1/genome3d//HiC-Pro_3.1.0/scripts/Makefile:181: hic_qc] Error 1

Script2 generated by Hi-C Pro is the following:

#!/bin/bash

#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 48:00:00
#SBATCH --mem-per-cpu=16G
#SBATCH -p batch
#SBATCH --partition=cpu

#SBATCH --mail-user=
#SBATCH --mail-type=end
#SBATCH --job-name=HiCpro_s1_HiC-pro_T47D_PARP1
#SBATCH --export=ALL
#SBATCH --array=1-6

cd $SLURM_SUBMIT_DIR

make --file /hpc/home/roberto.ferrari1/genome3d//HiC-Pro_3.1.0/scripts/Makefile CONFIG_FILE=/hpc/archive/G_BIOCOMP/roberto/config-hicpro.txt CONFIG_SYS=/hpc/home/roberto.ferrari1/genome3d//HiC-Pro_3.1.0/config-system.txt all_persample 2>&1

Structure of the samples:

ls -ltr ../../HiC-pro/mydata/sample*/

../../HiC-pro/mydata/sample2/:
total 28708752
-rwxr-xr-- 1 G_BIOCOMP 14451050564 Nov 5 14:26 T47_T0_R1.fastq.gz
-rwxr-xr-- 1 G_BIOCOMP 14946702446 Nov 5 14:30 T47_T0_R2.fastq.gz

../../HiC-pro/mydata/sample3/:
total 25940376
-rwxr-xr-- 1 G_BIOCOMP 13072037358 Nov 5 14:31 T47_T60_R1.fastq.gz
-rwxr-xr-- 1 G_BIOCOMP 13490903888 Nov 5 14:33 T47_T60_R2.fastq.gz

../../HiC-pro/mydata/sample5/:
total 33720200
-rwxr-xr-- 1 G_BIOCOMP 17000553722 Nov 5 14:32 siPP_T0_R1.fastq.gz
-rwxr-xr-- 1 G_BIOCOMP 17528922940 Nov 5 14:34 siPP_T0_R2.fastq.gz

../../HiC-pro/mydata/sample6/:
total 32938448
-rwxr-xr-- 1 G_BIOCOMP 16565341213 Nov 5 14:32 siPP_T60_R1.fastq.gz
-rwxr-xr-- 1 G_BIOCOMP 17163617354 Nov 5 14:34 siPP_T60_R2.fastq.gz

../../HiC-pro/mydata/sample4/:
total 53801888
-rw-r--r-- 1 G_BIOCOMP 27136445038 Nov 5 14:33 siCTRL_R1.fastq.gz
-rw-r--r-- 1 G_BIOCOMP 27956679823 Nov 5 14:35 siCTRL_R2.fastq.gz

../../HiC-pro/mydata/sample1/:
total 39430184
-rw-r--r-- 1 G_BIOCOMP 19844584213 Oct 4 2022 T0_HiC_R1.fastq.gz
-rw-r--r-- 1 G_BIOCOMP 20531918213 Oct 4 2022 T0_HiC_R2.fastq.gz

any help?

Thanks,
R

[robertferr]

More first script of HiC-Pro only resulted in bowtie2 alignment for first three files:

(genome3d) [r@ui01 HiCPro_PARP1]$ ls bowtie_results/bwt2/
sample1 sample2 sample3