Question: problem with bowtie2 allignment
0
gravatar for khandaud15
8 days ago by
khandaud150
khandaud150 wrote:

Can any help me out with this problem. I am using bowtie2 to allign my fastq files to reference genome hg38. every time when I run the following Command i am getting and error (ERR): bowtie2-align died with signal 9 (KILL)".

command I am using :

bowtie2 -p 24 -x hg38 -X 2000 -1 R-CA-013-2-14_S3_R1.fastq.gz -2 R-CA-013-2-14_S3_R2.fastq.gz -S R-CA-013-2-14_S3 --no-unal

I would really appreciate if anyone could let me know whats the error about? sorry for the english. thanks

rna-seq bowtie2 • 133 views
ADD COMMENTlink modified 7 days ago • written 8 days ago by khandaud150

How much memory do you have available? And did you try with fewer threads, like -p 6?

ADD REPLYlink written 7 days ago by h.mon16k

Total of 50 gb memory and I tried using p as 6, still Getting the same error!!

ADD REPLYlink modified 7 days ago • written 7 days ago by khandaud150

Was bowtie2 already installed on this cluster (and know to work) or did you download the program (and compile?) yourself?

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax51k

It was already installed on cluster! All I did was module load bowtie2 And wrote my command

ADD REPLYlink written 7 days ago by khandaud150

Are you also using a job scheduling program then? If you are on a cluster you may not be allowed to run programs outside the scheduler. Is the above command only thing you typed in? You may need to talk with your local IT support to find out what is the proper way of submitting jobs on your cluster.

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax51k

Hi! So I am running this command on HPC cluster which has 32 cores!!

ADD REPLYlink written 7 days ago by khandaud150

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

@h.mon asked how much "memory" you have available?

ADD REPLYlink written 7 days ago by genomax51k

You can try to download the latest binary and run the command with it instead of the preinstalled one.

ADD REPLYlink written 7 days ago by ATpoint5.5k
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