problem with bowtie2 allignment
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
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How much memory do you have available? And did you try with fewer threads, like
-p 6?Total of 50 gb memory and I tried using p as 6, still Getting the same error!!
Was bowtie2 already installed on this cluster (and know to work) or did you download the program (and compile?) yourself?
It was already installed on cluster! All I did was module load bowtie2 And wrote my command
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.
Hi! So I am running this command on HPC cluster which has 32 cores!!
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.@h.mon asked how much "memory" you have available?
You can try to download the latest binary and run the command with it instead of the preinstalled one.
Did you build a reference genome index?
It shouldn't matter I believe, but the argument to
-Sis the name of your sam file so would be better to useR-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):