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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Fatal Error in call peaks when starting with tag aligns #109

Open easwaranramamurthy opened 6 years ago

easwaranramamurthy commented 6 years ago

Hello,

I am running into an error in call_peaks when I run the following command:

srun -p part1 --mem=1G --pty /bin/bash

bds_scr job_1 /home/username/job_1.log -s slurm /path/to/atac_dnase_pipelines/atac.bds -q part1 -nth 4 -species mm10 -se -enable_idr -title job_1 -tag1 /path/to/peaks/sample_1/align/rep1/sample_1.trim.nodup.tagAlign.gz -tag2 /path/to/peaks/sample_2/align/rep1/sample_2.trim.nodup.tagAlign.gz -tag3 /path/to/peaks/sample_3/align/rep1/sample_3.trim.nodup.tagAlign.gz -out_dir /path/to/peaks/job_1_IDR

I would greatly appreciate any help in debugging this issue. The log file is attached. job_1.log

Thank you.

-Easwaran

leepc12 commented 6 years ago

Can you increase memory for MACS2 (by adding -mem_macs2 20G to the command line) and try again?

some references: https://github.com/JuliaLang/julia/issues/14807 https://stackoverflow.com/questions/27825280/change-the-rlimit-nproc-in-linux