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Bismark Extract failed always ran out of memory after 8hrs. #662
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Assuming the human genome, and easy to work numbers, a single run of Bismark requires ~3 cores (at 100%) and ~14GB of RAM for a standard directional run, and 5 cores and ~20GB of RAM for a non directional run. Since you used Does that make sense? |
Thank you. |
Thank you so much for your reply. New Error: 2- bowtie2-align died with signal 9 (KILL) |
That still sounds like memory issues, what did you change? |
Bismark_mapping Failed, Run time 08:18:26, OUT_OF_MEMORY.
Please see code
bismark --genome_folder genomes/bismark -o bam/ --non_directional --parallel 8 --score_min L,-0.6,-0.6 -1 trimmed/${base1}_val_1.fq.gz -2 trimmed/${base2}_val_2.fq.gz
What am I doing wrong? I am running on a cluster using 16 nodes for the job submission.
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