Bowtie2-build not working
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17 months ago
Raygozak ★ 1.4k

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 • 1.2k views
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17 months ago
Raygozak ★ 1.4k

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

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I have 64 GB

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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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