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
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'
... || 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.