JUM (v2.0.2 and up) stops and get killed at a certain step
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6 weeks ago

Dear all, I'm using JUM pipeline (https://github.com/qqwang-berkeley/JUM/wiki/3.1.-Manual-running-JUM-(v2.0.2-and-up)) to analyze alternative splicing RNA-sequencing but the bash code stops and get killed at this step:

    process_sortedbam () {
sortfile=$1; bamfiletobed=${sortfile%_sorted.bam}.bed;
bamsortedbed=${sortfile%_sorted.bam}.sorted.bed; intersect_bam_long_intron=${sortfile%_sorted.bam}"_"intersect_long_intron.txt;
intersect_bam_short_intron1=${sortfile%_sorted.bam}"_"intersect_short_intron1.txt; intersect_bam_short_intron2=${sortfile%_sorted.bam}"_"intersect_short_intron2.txt;
bedtools bamtobed -i $sortfile >$bamfiletobed;
sort -k1,1 -k2,2n $bamfiletobed >$bamsortedbed;
intersectBed -a $bamsortedbed -b output_long_intron_sorted.gff -sorted -wa -u -f 1 >$intersect_bam_long_intron
intersectBed -a $bamsortedbed -b output_short_intron1_sorted.gff -sorted -wa -u -f 1 >$intersect_bam_short_intron1
intersectBed -a $bamsortedbed -b output_short_intron2_sorted.gff -sorted -wa -u -F 1 >$intersect_bam_short_intron2
}


Exact error:

Killed                sort -k1,1 -k2,2n $bamfiletobed >$bamsortedbed


Has anyone have any experience with this error or know what should I do? I'm guessing it might be a CPU error as it gets killed but more than that, not sure. I'm working with a 16 threads system and once used all and other times just 14 of them, but it gets killed anyway. I should mention that JUM runs all the samples (6 in my case) in parallel.

Code I'm using:

bash /path/JUM_2.0.2_multi/JUM_A.sh --Folder /path/JUM_2.0.2_multi --JuncThreshold 5 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --IRthreshold 5 --Readlength 101 --Thread 16 --Condition1SampleName cntrl1,cntrl2,cntrl3 --Condition2SampleName treat1,treat2,treat3


Thanks.

alternative_splicing RNAseq AS JUM • 394 views
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Look into if you are running out of RAM. Using less cores may actually help in that case since RAM requirements may be reduced.

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I reduced to 8, but it didn't work. Still get killed at the same step. The developers told me to run the script on non-parallel mode but there isn't any bash code or other guide that I can switch it to that mode.

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Try --Thread 1 then.

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They sent a non parallel code as it was analyzing all my samples in parallel mode. My system wasn't able to do that.