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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Error in reads alignment #496

Closed LlChangSub closed 2 years ago

LlChangSub commented 2 years ago

hello, I download HiC-Pro from github, version3.1.0, and download demo test data, but the step "Bowtie2 alignment step2 ..." always getting wrong, The error information is as follows Run HiC-Pro 3.1.0

Mon Nov 15 09:57:54 CST 2021 Bowtie2 alignment step1 ... Logs: logs/dixon_2M_2/mapping_step1.log Logs: logs/dixon_2M/mapping_step1.log

Mon Nov 15 09:58:57 CST 2021 Bowtie2 alignment step2 ... Logs: logs/dixon_2M_2/mapping_step2.log Exit: Error in reads alignment - Exit make: *** [biosoft/hicpro/HiC-Pro-3.1.0/bin/../scripts//Makefile:101: bowtie_local] Error 1 can you tell me how to solve this problem? Thank you!

nservant commented 2 years ago

Hi, Please, have a look at the logs/dixon_2M_2/mapping_step2.log file. Do you have a clear error message ? Best

TonFerreira commented 2 years ago

Hi, I have a similar issue in "Combine R1/R2 alignment files ..."

slurmstepd: error: Job 40131247 exceeded memory limit (204802220 > 204800000), being killed slurmstepd: error: Exceeded job memory limit

I put in my config-hicpro file: N_CPU = 8 SORT_RAM = 12000M

And in my slurm file:

SBATCH -c 16

SBATCH --mem=200000

SBATCH -N 1

I have read that Sort_bam x CPUs will give the memory limits of Hi-C Pro to work: so 8 CPUs x 12 gb = 96 gb, but apparently, this did not work.

In my mapping_combine.log apparently there is no error: "/usr/local/anaconda/bin/samtools sort -@ 8 -m 12000M -n -T tmp/hiC_ppufv02_R2_ppufv.p_ctg_v1 -o bowtie_results/bwt2/rawdata/hiC_ppufv02_R2_ppufv.p_ctg_v1.bwt2merged.sorted.bam bowtie_results/bwt2/rawdata/hiC_ppufv02_R2_ppufv.p_ctg_v1.bwt2merged.bam"

Inside the bwt2 folder, there are two bam files, with one with 24 gb... But the script did not run after that...