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

[farzaneafzali]

Hi, The JUM_A.bash 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

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. 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

Does anyone know what might be wrong and how can I fix it please? Thanks.

[qqwang-berkeley]

Hi,

There are two possibilities:

1) the RAM can not handle the parallel processing mode of JUM_A. 2) there is not enough space in /tmp directory on your working computer/cluster for the sort command.

Both issues can be solved. let's try one first. For now, could you try the attached modified JUM_A.sh script and let me know if it solves the issue (just run the JUM_A_non_parallel.sh attached exactly as you run JUM_A.sh. It is just the name of the script is different.)?

Let me know.

Best,

Qingqing

On Tue, Aug 16, 2022 at 7:29 PM farzaneafzali @.***> wrote:

Hi, The JUM_A.bash 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

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. 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.

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[farzaneafzali]

Hi Qingqing, Thanks for replying back. I just can't find your attached file. Neither here nor in email. Maybe it didn't come through?!

Best, Farzaneh

[farzaneafzali]

Hi @qqwang-berkeley Can you please send the script again? I can't find it. Thanks so much

[qqwang-berkeley]

Could you please provide a personal email address? Turns out that I can’t attach files with the GitHub address. Thank you!

On Thu, Aug 18, 2022 at 8:52 AM farzaneafzali @.***> wrote:

Hi @qqwang-berkeley https://github.com/qqwang-berkeley Can you please send the script again? I can't find it. Thanks so much

— Reply to this email directly, view it on GitHub https://github.com/qqwang-berkeley/JUM/issues/40#issuecomment-1219455809, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ6PW6V444SXQTRDO2SSDDVZYWYTANCNFSM56XR7MVA . You are receiving this because you were mentioned.Message ID: @.***>

[farzaneafzali]

@qqwang-berkeley Of course. Here it is: farzaneafzali@gmail.com

Thank you!

[farzaneafzali]

@qqwang-berkeley Hi Qingqing, Just wanted to update you that this part finished successfully with non-parallel code. Thanks so much for your help, Farzaneh