The task seem to run fine up to what I think should be the end:
Number of designs excluded because the maximum of designs per exon was exceeded = 19100 Number of designs excluded because their nucleotide composition was too invariable or contained TTTTT = 8745692 Number of designs excluded because they did not hit any exon = 80373408 Number of designs excluded because they did not hit any gene = 7347674 Number of designs excluded because they hit multiple targets or none = 409564 Number of designs excluded because they were not located in a coding sequence = 3844194 Number of designs that hit a specific target = 4263656 Number of successful designs = 4244556 Number of total possible designs = 104984188
But it just remained stuck there for something like 2 days (I see it consuming a single CPU) and I didn't see the number for missing genes. My shell automatically closed due to inactivity, so I couldn't see any final error. The output files in the working dir seem untouched during that entire 2 day period.
I was trying to generate a full genome screen for female naked mole rat (make_database seemed to run successfully without any issue):
docker run -v ${PWD}/data:/data -v ${PWD}/var/www:/var/www boutroslab/cld_docker cld --task=end_to_end --output-dir=/data/ --parameter-file=/data/params/trail_parameters.txt --gene-list=/data/params/nmr_full_genome.txt --lib-size=300000 --cov=5 -library_name=ds20220908_full --5-prime=A --3-prime=AThe task seem to run fine up to what I think should be the end:
Number of designs excluded because the maximum of designs per exon was exceeded = 19100 Number of designs excluded because their nucleotide composition was too invariable or contained TTTTT = 8745692 Number of designs excluded because they did not hit any exon = 80373408 Number of designs excluded because they did not hit any gene = 7347674 Number of designs excluded because they hit multiple targets or none = 409564 Number of designs excluded because they were not located in a coding sequence = 3844194 Number of designs that hit a specific target = 4263656 Number of successful designs = 4244556 Number of total possible designs = 104984188But it just remained stuck there for something like 2 days (I see it consuming a single CPU) and I didn't see the number for missing genes. My shell automatically closed due to inactivity, so I couldn't see any final error. The output files in the working dir seem untouched during that entire 2 day period.