JUM (v2.0.2 and up) stops and get killed at a certain step
0
0
Entering edit mode
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
ADD COMMENT
0
Entering edit mode

Look into if you are running out of RAM. Using less cores may actually help in that case since RAM requirements may be reduced.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Try --Thread 1 then.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1845 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6