Empty output using ont_dorado_drna004 with the conda version

[lborcard]

Hi,

I am using the latest version of claire3_rna with conda and although the output is not indicating any error:

[COMMAND] //02_analysis/Clair3-RNA/run_clair3_rna --bam_fn es182_sup.sorted.bam --ref_fn /ncbi_dataset/data/rna.fna --threads 15 --platform ont_dorado_drna004 --output_dir /02_analysis/clair3_rna 

[INFO] --include_all_ctgs not enabled, use chr{1..22} and {1..22} by default

The output is empty and does not contain any .vcf file. I get the folder tree but all folders are empty.

tmp/
├── candidates
├── phased_output
│   ├── phased_bam
│   └── phased_vcf
├── pileup_output
└── split_beds

Do you need an aligned .bam file or only the output of dorado? I am using an aligned bam file mapped with minimap2 to the same reference that I am using now.

best,

Loïc

[zhengzhenxian]

Hi @lborcard,

Could you share the log file (run_clair3_rna.log) in your output directory for us to pinpoint the issue?

Also, If you are calling variants in non-human data, please add the --include_all_ctgs option.