Question: err: bowtie2-align exited with value 139
gravatar for Roger
13 months ago by
Roger0 wrote:

Hi there,

I'm trying to align my reads to a reference genome and I got this error (using the attached line). Reading previous comments I've seen that the last Bowtie version (2.3.4) should fix this problem. However, I'm using this version and I got the same error. I've also read it has something to do with my free-g screenshot. Can you help me, please? I'm quite new at I don't know what's going on!

$ bowtie2 --local --trim5 11 -x mm9 -U read1.barcoded.fastq.gz -S example.sam

version: Bowtie 2 version by Ben Langmead ...

free -g test

Thanks in advance!

alignment • 414 views
ADD COMMENTlink modified 13 months ago by RamRS25k • written 13 months ago by Roger0

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLYlink written 13 months ago by RamRS25k

Sorry, and thank you!

ADD REPLYlink written 13 months ago by Roger0
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