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Kallisto Indexing runs but produces no data #459

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arese001 opened this issue Sep 11, 2024 · 1 comment
Open

Kallisto Indexing runs but produces no data #459

arese001 opened this issue Sep 11, 2024 · 1 comment

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@arese001
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I can load my fasta and run the indexing function fine, but it simply produces nothing. The outpout looks like below in my terminal:

[build] loading fasta file Homo_sapiens.GRCh38.cdna.all.fa
[build] k-mer length: 31
[build] counting k-mers ... done.
[build] building target de Bruijn graph ... done
[build] creating equivalence classes ... done
[build] target de Bruijn graph has 0 contigs and contains 0 k-mers

The inside of the indexed file appears like:

0a00 0000 0000 0000 1f00 0000 0000 0000
0000 0000 0000 0000 0000 0000 0000 0000
0000 0000 0000 0000

@Yenaled
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Yenaled commented Sep 11, 2024

Can you check if your Homo_sapiens.GRCh38.cdna.all.fa file actually contains anything?

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