Error while parsing gtf

[asundaresan1]

Description of the bug

Hello,

I am getting the follwoing error when i run tf activity pipeline

Command output:
[1] "Reading genes.gtf elements of type gene"
[1] "Found 0 features"

Command error:
[1] "Reading genes.gtf elements of type gene"
[1] "Found 0 features"
gene_id is not a valid field

I am using Rat ensembl GTF.
Another issue is I am not able to use narrowPeak files. I had to rename them to broadPeak in order to process them.

Command used and terminal output

nextflow run nfcore/pipelines/tfactivity/dev/workflow \
            --input samplesheet.csv \
            --outdir ./results \
            -profile  singularity \
            --counts hisat.counts_for_tfactivity.csv \
            --counts_design rnaseq_design.csv \
            -config genome.config \
            --genome rat-ensembl-rn6-r102 \
            --taxon_id 10116

Relevant files

No response

System information

No response

[nictru]

Hey, could you provide more detailed error information? E.g. the .nextflow.log file? It's very hard to find out where in the pipeline this error occurred without more information.

[asundaresan1]

error.log
Hi @nictru ,

Attached is the nextflow.log

Thanks!