thread 'main' panicked

[beaLando]

Hello,
This package seems very useful, but I get an error when running it.

I have installed the package via "conda install gxf2bed -c bioconda" as suggested, after creating an environment specifically for the package.

After gxf2bed starts to run, I get an error and this is the output:

GXF2BED

Fastest GTF/GFF-to-BED converter chilling around.
Repository: https://github.com/alejandrogzi/gxf2bed
Feel free to contact the developer if any issue/bug is found.
Version: 0.2.4

2025-01-16T09:17:24.270Z INFO [gxf2bed] Args { gxf: "data/GCF_000001735.4_TAIR10.1_genomic_noheaderFilt2.gff", output: "data/GCF_000001735.4_TAIR10.1_genomic_noheaderFilt2.bed", threads: 16, parent: "transcript", child: "exon", feature: "transcript_id" }
2025-01-16T09:17:24.274Z INFO [gxf2bed] Using 16 threads
2025-01-16T09:17:26.914Z INFO [gxf2bed] 53828 records parsed
thread 'main' panicked at src/main.rs:209:36:
called Option::unwrap() on a None value
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

As a result, the bed file is written, but it is empty. By searching the error I see it is possibly a rust error and that maybe it has to do with the input file not meeting some conditions, but maybe I am wrong. I am really not familiar with rust. I have tried to reduce the number of threads, running gxf2bed on a server with more threads, and use different gtf/gff files as input, but the situation did not change.

I have also tried to run a gff2bed conversion using the package bedops and it seems like there are lines that are "too long" in the input file. My version of conda is 23.7.3 and I am working with WSL.

Thank you,
Bea

[alejandrogzi]

Hi @beaLando

Thanks for reporting this. I just published a new version fixing some bugs. Could you please give it a try and see if the error persists? If the error persist, please send your file to have a look.

Cheers,
Alejandro