8000 Output contains only * with no counts · Issue #26 · kamimrcht/REINDEER · GitHub
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Output contains only * with no counts #26

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tbenavi1 opened this issue Oct 2, 2024 · 0 comments
Open

Output contains only * with no counts #26

tbenavi1 opened this issue Oct 2, 2024 · 0 comments

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@tbenavi1
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tbenavi1 commented Oct 2, 2024

Hello,

I created a Reindeer index on the T2T genome, and then queried the genome against the index in order to get the counts of all the kmers. The commands I ran were:

bcalm -in chm13v2.0.fasta -kmer-size 31 -abundance-min 1 -nb-cores 32
Reindeer --index -f fof_unitigs.txt -o quick_out -t 32
Reindeer --query -q chm13v2.0.fasta -l quick_out -o quick_out/result.txt

However, for most of the chromosomes the result file only had "*". I have uploaded the reindeer index folder and result file here: https://drive.google.com/drive/folders/1P3ABKTFboLuiQ_YjWfsmz-Q3kLXWCfpL?usp=drive_link

Chromosomes 17, 18, and M have the expected output. I did run a query on a subset of chromosome 1, and it did seem to produce the correct output. I'm not sure if there is some error with really long sequence lengths. Thanks for any suggestions.
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