Question: problem with bowtie2 allignment
0
gravatar for arshil
9 weeks ago by
arshil0
arshil0 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 • 245 views
ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 9 weeks ago by arshil0

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

ADD REPLYlink written 9 weeks ago by h.mon19k

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

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by arshil0

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

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax55k

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

ADD REPLYlink written 9 weeks ago by arshil0

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 9 weeks ago • written 9 weeks ago by genomax55k

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

ADD REPLYlink written 9 weeks ago by arshil0

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 9 weeks ago by genomax55k

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

ADD REPLYlink written 9 weeks ago by ATpoint7.4k

Did you build a reference genome index?

It shouldn't matter I believe, but the argument to -S is the name of your sam file so would be better to use R-CA-013-2-14_S3.sam.

Even better would be to let bowtie write to stdout and convert to bam on the fly (requiring a reasonably recent version of samtools):

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 --no-unal | satmtools sort -o R-CA-013-2-14_S3.bam
ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by WouterDeCoster32k
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