Segmentation fault with HOMER
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7 months ago
pixie@bioinfo ★ 1.4k

Hello, I am analyzing captureHiC data with HOMER by using the findHiCInteractionsByChr.pl module. I am running it as an sbatch script with the following parameters:

findHiCInteractionsByChr.pl $folder/ -res 2000 -pvalue 0.05 -zscore 0.5 -cpu 24 >$output/basename \$folder_Interactions_byChr.txt"


However, I keep getting these segmentation faults in my error file. Although it gives me a list of significant loops, I do not know if the list is complete. Can anyone throw some light on this issue ? Is it because of memory problem ?

Average interaction count in regions = 153.4 +/- 180.2 (143.4 without outliers)
Chr6 (avg coverage: 143.4, coverage ratio=1.051)

Regions with too many or too few reads: 2.43%
Total Significant Interactions: 6354
Reporting log2 values
Segmentation fault
Regions with too many or too few reads: 8.09%
Total Significant Interactions: 3350
Reporting log2 values
Segmentation fault

homer HiC • 228 views