mode(counts) %in% "numeric" is not TRUE issue when commenting strip_version does not work

[C-Pauli]

Hi I've ran into the same issue and commenting out the strip_version has not helped. I'm running an NCBI genome cds file and annotation gff. Neither the GFF or the GTF seem to work even when grep -v genes that it has specific problems with.

"Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
some transcripts have no "transcript_id" attribute ==> their name
("tx_name" column in the TxDb object) was set to NA
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID, :
the transcript names ("tx_name" column in the TxDb object) imported
from the "transcript_id" attribute are not unique
'select()' returned 1:many mapping between keys and columns
Error in dmDSdata(counts = counts, samples = coldata) :
mode(counts) %in% "numeric" is not TRUE
Calls: dmDSdata -> stopifnot
Execution halted
[Thu Sep 9 01:51:02 2021]
Error in rule de_analysis:
jobid: 0
output: de_analysis/results_dge.tsv, de_analysis/results_dge.pdf, de_analysis/results_dtu_gene.tsv, de_analysis/results_dtu_transcript.tsv, de_analysis/results_dtu_stageR.tsv, merged/all_counts_filtered.tsv, merged/all_gene_counts.tsv
shell:

/epi2melabs/differential-expression/pipeline-transcriptome-de/scripts/de_analysis.R

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /epi2melabs/differential-expression/.snakemake/log/2021-09-09T015044.982826.snakemake.log"

GCF_900626175.1_cs10_genomic.gff.gz

GCF_900626175.1_cs10_cds_from_genomic.fna.gz

Originally posted by @C-Pauli in #18 (comment)