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relipmoc / skewer

MIT License
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segfault on -m mp #20

Closed sklages closed 6 years ago

sklages commented 9 years ago

Hi,

I compiled skewer wihout any issues on our home-made linux system.

Running skewer then on two 55GB fastq files results in a segfault after a few seconds.

skewer -m mp -i mpg_L4499-4_MySuperProjectXXX_AGTCAA_L002_R1_001.fastq mpg_L4499-4_MySuperProjectXXX_AGTCAA_L002_R2_001.fastq
Parameters used:
-- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y):   AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
-- junction adapter sequence (-j):  CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
-- maximum error ratio allowed (-r):   0.100
-- maximum indel error ratio allowed (-d):   0.030
-- minimum read length allowed after trimming (-l):   18
-- file format (-f):    Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for junction adapter detection (-k): 0
-- redistribute reads based on junction information (-i):   yes
Fri Jun 12 11:06:47 2015 >> started
|>                                                 | (0.02%)Segmentation fault

Omitting the second fastq file does not result in a segfault.

This is 256GB / 48 core machines. Ressources should suffice .. any idea?

best, Sven

relipmoc commented 9 years ago

Could you send me part of the data that cause this segmentation fault?