Salmon index issue
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8 weeks ago
Andrea ▴ 10

I'm trying to construct the reference for Salmon, but the process stopped with this error:

the commandis:

salmon index -t CRCH38_and_decoys.fa.gz -d decoys.txt -i GRCh38_salmon_index --gencode

the last part of the error is:

[2024-02-19 12:14:55.227] [puff::index::jointLog] [warning] Entry with header [ENST00000634174.1|ENSG00000282732.1|OTTHUMG00000191398.1|OTTHUMT00000487783.1|ENST00000634174|ENSG00000282732|28|unprocessed_pseudogene|], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)

[2024-02-19 12:15:56.790] [puff::index::jointLog] [warning] Removed 882 transcripts that were sequence duplicates of indexed transcripts. [2024-02-19 12:15:56.792] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the --keepDuplicates flag [2024-02-19 12:15:56.919] [puff::index::jointLog] [info] Replaced 151122967 non-ATCG nucleotides [2024-02-19 12:15:56.919] [puff::index::jointLog] [info] Clipped poly-A tails from 2034 transcripts Killed

it could be a problem of CPU memory?

Thanks

Salmon RNAseq • 357 views
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How much memory is available?

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I have a laptop with 16 Gb

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I just checked my logs, and a full genome-decoyed GRCh38 with Ensembl 101 annotations took 15GB to create. Possible that you simply do not have enough, since also other applications need some memory on your machine.

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you can download prebuilt indices with refgenie

https://refgenie.databio.org/en/latest/

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