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.
Killedvery likely means something to do with memory, yes.
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.
Update: It was a problem with memory. I used another machine with higher memory access and the process was completed.