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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Assign alignments to restriction fragments #582

Closed LHXqwq closed 5 months ago

LHXqwq commented 1 year ago

Wed Jun 28 17:31:17 CST 2023 Assign alignments to restriction fragments ... Logs: logs/W2-6/mapped_2hic_fragments.log make: *** [/xtdisk/zhangzhh_group/lizijian/HiC-Pro/bin/../scripts//Makefile:152: mapped_2hic_fragments] Error 137

(base) [lizijian@vmloginb2 W2-6]$ tail mapped_2hic_fragments.log

729500000

729600000

729700000

729800000

729900000

730000000

730100000

Sorting valid interaction file ...

LANG=en; sort -T tmp -k2,2V -k3,3n -k5,5V -k6,6n -o hic_results/data/W2-6/W2-6_val_genome.bwt2pairs.validPairs hic_results/data/W2-6/W2-6_val_genome.bwt2pairs.validPairs /xtdisk/zhangzhh_group/lizijian/HiC-Pro/scripts/hic.inc.sh: line 86: 4365 Killed sort -T tmp -k2,2V -k3,3n -k5,5V -k6,6n -o hic_results/data/W2-6/W2-6_val_genome.bwt2pairs.validPairs hic_results/data/W2-6/W2-6_val_genome.bwt2pairs.validPairs

Hello, I have an error in the step of assigning alignments to restriction fragments, what is the possible reason？

nservant commented 5 months ago

Look like a memory issue ... I guess the 'sort' command is requiring too much memory