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nf-core / tfactivity

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
https://nf-co.re/tfactivity
MIT License
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Error while parsing gtf #17

Open asundaresan1 opened 2 months ago

asundaresan1 commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

error.log Hi @nictru ,

Attached is the nextflow.log

Thanks!