err: bowtie2-align exited with value 139

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5.2 years ago

Roger • 0

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 memory...here my free-g screenshot. Can you help me, please? I'm quite new at that...so 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 2.3.4.3 by Ben Langmead ...

free -g test

Thanks in advance!

alignment • 1.9k views

ADD COMMENT • link updated 5.2 years ago by Ram 43k • written 5.2 years ago by Roger • 0

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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.
code_formatting

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)