I am trying to create an index file with kallisto for mapping RNA seq data. OS of my laptop is Ubuntu 18.04 and I am working on its bash.

Version $ kallisto kallisto 0.46.2

I downloaded reference cDNA data from: ftp://ftp.ensembl.org/pub/release-99/fasta/homosapiens/cdna/Homosapiens.GRCh38.cdna.all.fa.gz

Then I run the command:

$ kallisto index -i kallisto.idx Homo_sapiens.GRCh38.cdna.all.fa

Also tried:

$ kallisto index --index=kallistoidx Homosapiens.GRCh38.cdna.all.fa

Then I got the following error:

[build] loading fasta file homosapiens/Homosapiens.GRCh38.cdna.all.fa

[build] k-mer length: 31

[build] warning: clipped off poly-A tail (longer than 10)

    from 1431 target sequences

[build] warning: replaced 5 non-ACGUT characters in the input sequence

    with pseudorandom nucleotides

[build] counting k-mers ... Forced termination

I think kallisto can work without large memory and that is why I am trying. Could you please advise me how to fix this.

Thank you

Kallisto is not Bioconductor software and so this isn’t an appropriate place to post.