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Bowtie2-build not working

Hi, i'm trying to build an index using bowtie2 (Yes it has to be bowtie2), but it just bails out and generates .tmp files with the index names.

I have tried the conda based binaries and downloading the github source and compiling it. It would be useful if there's a fix for this that someone knows about.

Thanks

bowtie2-buid index
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written by Raygozak Raygozak

1 answer

I just checked and all this time I was using --threads 4 and other amount of threads, and then tried it without threads and it's working now. I'll report it to the developers.

Edit: as a temporary solution I downloaded the precompiled binaries from the github repo, and they work fine under ubuntu 22.04.

Thanks

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written by Raygozak Raygozak

What was the error? Did your job get killed due to memory shortage?

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written by ATpoint ATpoint

I have 64 GB

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written by Raygozak Raygozak

No error, just exits.

No, I restarted and tried again with most of the memory available and I had the same problem. It never wen't upwards of 20% memory usage and it crashed again.

Idk where the bug is but it clearly affects bowtie.

Edit: This seems to happen only on Ubuntu 22.04 I tested it on Ubuntu 20.04 and works fine, so yeah maybe it's a library but it is real. Haven't tested it on other versions of ubuntu.

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written by Raygozak Raygozak

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