At the parse_gff.R stage of the pipeline, I recurrently encountered the following messages and error related to a mismatch between my accession ranking file and annotation file:
Checking that all gene and transcript types are included in ranking.
Note: The following accession types are present in the ranking file but not used in this GFF:
- primary_miRNA
Error: Accession ranking file does not match the GFF annotation.
Ranking file: /mnt/BSTORE/almca2/software/skipper/annotations/accession_type_ranking_2.txt
GFF file: /mnt/BSTORE/almca2/Genomes/Mus_musculus.GRCm39.116.filtered.gff3.gz
Execution halted
Since the source of the mismatch was not reported in the error message, this required some investigation! After some poking around, it seems this occurred because some of my transcript types were 'NA', which I had not included as a category in my ranking file. An easy oversight to correct on my part, but it would be helpful to add an error message for the contents of missing_transcript_types as well as missing_gene_types during this check in parse_gff.R.
P.s. Thank you for creating this pipeline and for the detailed documentation :) I am a total snakemake rookie, so all the work you've put in has been incredibly helpful to me.
At the parse_gff.R stage of the pipeline, I recurrently encountered the following messages and error related to a mismatch between my accession ranking file and annotation file:
Since the source of the mismatch was not reported in the error message, this required some investigation! After some poking around, it seems this occurred because some of my transcript types were 'NA', which I had not included as a category in my ranking file. An easy oversight to correct on my part, but it would be helpful to add an error message for the contents of
missing_transcript_typesas well asmissing_gene_typesduring this check in parse_gff.R.P.s. Thank you for creating this pipeline and for the detailed documentation :) I am a total snakemake rookie, so all the work you've put in has been incredibly helpful to me.