SALMON Index build Process Killed!
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21 days ago
Soumajit ▴ 30

Hello,

I was trying to create an decoy-aware index with Salmon (v1.4.0). So I used primary-assembly genome file and transcript file from Gencode library and followed the steps mentioned in the combine-lab.github.io/alevin-tutorial/2019/selective-alignment. Concatenated transcript file with genome to create gentrome.fa.gz. Then tried to create the index with following script,

salmon index -t gentrome.fa.gz -i IndexSalmonDecoyAware --decoys decoys.txt -k 31 --gencode

It starts with counting k-mers and then after sometime, it kills the process.

[2023-01-18 10:53:10.587] [puff::index::jointLog] [info] Replaced 151,122,967 non-ATCG nucleotides

[2023-01-18 10:53:10.587] [puff::index::jointLog] [info] Clipped poly-A tails from 2,020 transcripts Killed

No informtion of error or nothing else. I have a machine with 16gb memory. Does anyone think that this abrupt stop is because of limited free RAM? I was checking task manager and it looked like during the killing process, there were still around 3 gb of RAM free.

Any help would be highlt appreciated. Thanks a lot.

salmon index mapping • 319 views
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Killed very likely means something to do with memory, yes.

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You appear to be using an older version of salmon. Current is v.1.9. Upgrade if you can.

Prebuilt indexes (decoy aware as well) are available for model organisms here: http://refgenomes.databio.org/ You could download them.

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Update: It was a problem with memory. I used another machine with higher memory access and the process was completed.

Thanks.

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