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Kallisto process killed or computer freezes while indexing #405

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hkarakurt8742 opened this issue Oct 23, 2023 · 1 comment
Open

Kallisto process killed or computer freezes while indexing #405

hkarakurt8742 opened this issue Oct 23, 2023 · 1 comment

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@hkarakurt8742
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Hello,
I am trying to create index for "Homo_sapiens.GRCh38.dna.primary_assembly.fa" from Ensembl. I installed Kallisto using conda (kallisto 0.48.0) and tried to index using kallisto index -i Homo_sapiens.idx Homo_sapiens.GRCh38.dna.primary_assembly.fa and the process is killed.
Then I installed kallisto 0.50 from source and tried the same using -t parameter as 10, 8, 6, 2 and 1. For all of them, the computer freezes due to memory loss.
My computer has 48 GB of RAM and Intel i7-10700F CPU. As I know indexing should not use such memory but I could not solve it.
What might be the problem here?

Thank you in advance.

@Yenaled
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Yenaled commented Oct 23, 2023

You're indexing the genome, not the transcriptome. Kallisto requires you to index the transcriptome. Homo_sapiens.GRCh38.dna.primary_assembly.fa is a genome FASTA file, not a transcriptome FASTA file.

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