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R2Dtool annotate error #5

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liftedlink opened this issue Nov 21, 2024 · 3 comments
Open

R2Dtool annotate error #5

liftedlink opened this issue Nov 21, 2024 · 3 comments

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@liftedlink
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liftedlink commented Nov 21, 2024

Hello, excited to use the R2Dtool. I am having trouble with the annotate function. I am running on a linux server, and compiled on rust 1.76.0
Command used:
r2d annotate --gtf Homo_sapiens.GRCh38.113.gtf --input r2_bed_m6a.bed > test.bed

Output error:
thread 'main' panicked at src/annotate.rs:185:47:
called Result::unwrap() on an Err value: ParseIntError { kind: InvalidDigit }
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

I am able to reproduce this error on my macbook and while using the test data.

@liftedlink liftedlink changed the title R2Dtool annotate error ls R2Dtool annotate error Nov 21, 2024
@liftedlink
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I should note, the "splice_sites_map.txt" file output is produced.

@pre-mRNA
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pre-mRNA commented Dec 8, 2024

Hi, can you please share a sample of the input data being used?

@liftedlink
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Here is the bed file I was using.

I have been able to use the deprecated Rscripts and have found that the outputs work fine with the remaining tools. Seems to just be an issue with the rust built annotate function.
r2_bed_m6a.txt

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