msbentsen
commented
2 years ago I think the error already says it:
2021-09-09 12:49:38 (23442) [ERROR] Query feature(s) ['gene'] not found in gtf
So the third column of the .gtf contains the type of feature e.g. 'gene', 'exon', 'transcript' etc. The query feature 'gene' does not exist in this column. If you use --debug with UROPA, the log will contain a line with [DEBUG] - Features in gtf:, which will show the available features. Can you have a look at that and see if 'gene' is within these options?
I am following the examples on the webpage. It resulted in error.
The configuration that I used: { "queries": [ {"feature":"gene", "distance":3000, "feature.anchor": "start", "show.attributes":"gene_name"}], "priority" : "False", "gtf": "Reference/Genome/Homo_sapiens/UCSC/hg38/Annotation/Genes.gencode/genes.gtf", "bed": "test2.bed" }
The following is the error message that I got from running the command uropa - i con2.json:
2021-09-09 12:48:58 (23442) [INFO] Started UROPA 4.0.2 2021-09-09 12:48:58 (23442) [INFO] Working directory: /users/xlixzcyn 2021-09-09 12:48:58 (23442) [INFO] Command-line call: /usr/local/anaconda3-2020/envs/uropa/bin/uropa -i con2.json 2021-09-09 12:48:58 (23442) [INFO] Reading configuration from commandline/input config 2021-09-09 12:48:58 (23442) [INFO] Preparing .gtf-file for fast access 2021-09-09 12:49:38 (23442) [INFO] Config key show_attributes was set to 'all'. All possible attributes are shown in output (['ccdsid', 'exon_id', 'exon_number', 'gene_id', 'gene_name', 'gene_status', 'gene_type', 'havana_gene', 'havana_transcript', 'level', 'ont', 'p_id', 'protein_id', 'tag', 'transcript_id', 'transcript_name', 'transcript_status', 'transcript_support_level', 'transcript_type', 'tss_id']) 2021-09-09 12:49:38 (23442) [ERROR] Query feature(s) ['gene'] not found in gtf 2021-09-09 12:49:38 (23503) [ERROR] Logger lost connection to queue - probably due to an error raised from a child process.