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sha-ked • 0
@87ffeb56
Last seen 9 months ago
Israel

Hi, I am having a problem in mapping subread with more than one thread. I am using SLURM workload manager in my High performance computing system. Whenever I use -T in Subread to map merged reads and detect junctions (using subjunc) I am coming across with an error I couldn't find on the internet I use Pear* tool to merge my paired reads together before mapping

Input:

sbatch -wrap 'subjunc -T 10 -B 10 -D 700 -I 1 -M 0 -i index -m 1 -p 1 -o merge.sam  -r merged.fastq.assembled.fastq --multiMapping --allJunctions --SAMoutput'

Output:

...
|| Start read mapping in chunk.                                                                       ||
||    0% completed, 0.4 mins elapsed, rate=34.1k reads per second              ||
||    6% completed, 1.0 mins elapsed, rate=35.8k reads per second              ||
||   13% completed, 1.6 mins elapsed, rate=35.9k reads per second             ||
||   20% completed, 2.2 mins elapsed, rate=35.9k reads per second             ||
subjunc: core-indel.c:1085: finalise_indel_and_junction_thread: Assertion `merged_body -> event_type == old_body -> event_type' failed.
/var/spool/slurmd/job1147399/slurm_script: line 4: 118457 Aborted                 subjunc -T 10 -B 10 -D 700 -I 1 -M 2 -i index -o ncan.sam -r merged.fastq.assembled.fastq --multiMapping --allJunctions --SAMoutput

If any of you have any advise and understand the error, please let me know. This happens only when I map merged reads, when I map paired reads alone it maps fine.

Slurm Subread • 308 views
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It probably gets killed by slurm, because it uses 10 cores while you requested one. At least on our HPC plain sbatch defaults to requesting a single core.

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