2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:74 - You are using dnaapler version 1.2.0
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:75 - Repository homepage is https://github.com/gbouras13/dnaapler
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:76 - Written by George Bouras: george.bouras@adelaide.edu.au
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:77 - Your input file is results/bsubtilis/assembly/assembly.fasta
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:78 - Your output directory  is results/bsubtilis/circularization
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:79 - You have specified 8 threads to use with MMseqs2
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:begin_dnaapler:80 - You have specified all gene(s) to reorient your sequence
2025-08-18 21:14:15.983 | INFO     | dnaapler.utils.util:check_mmseqs2_version:122 - Checking MMseqs2 installation.
2025-08-18 21:14:15.987 | INFO     | dnaapler.utils.util:check_mmseqs2_version:142 - MMseqs2 version found is 18.8cc5c
2025-08-18 21:14:15.987 | INFO     | dnaapler.utils.util:check_mmseqs2_version:156 - MMseqs2 version is ok.
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:check_pyrodigal_version:95 - Checking pyrodigal installation.
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:check_pyrodigal_version:106 - Pyrodigal version is v3.6.3
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:check_pyrodigal_version:107 - Pyrodigal version is ok.
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --input results/bsubtilis/assembly/assembly.fasta
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --output results/bsubtilis/circularization
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --threads 8
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --force False
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --prefix dnaapler
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --evalue 1e-10
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --autocomplete none
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --seed_value 13
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --ignore 
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --custom_db 
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.util:begin_dnaapler:85 - Parameter: --db all
2025-08-18 21:14:15.988 | INFO     | dnaapler.utils.validation:validate_input_all:113 - Checking that the input file results/bsubtilis/assembly/assembly.fasta is in FASTA or GFA format and has at least 1 entry.
2025-08-18 21:14:16.016 | INFO     | dnaapler.utils.validation:check_file_format:62 - results/bsubtilis/assembly/assembly.fasta is in FASTA format.
2025-08-18 21:14:16.047 | INFO     | dnaapler.utils.validation:validate_input_all:120 - results/bsubtilis/assembly/assembly.fasta has more than one entry.
2025-08-18 21:14:16.078 | INFO     | dnaapler.utils.validation:check_evalue:185 - You have specified an evalue of 1e-10.
2025-08-18 21:14:16.132 | INFO     | dnaapler.utils.external_tools:run:52 - Started running mmseqs easy-search results/bsubtilis/circularization/rotated_input.fasta /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/dnaapler/db/all_db results/bsubtilis/circularization/dnaapler_MMseqs2_output.txt results/bsubtilis/circularization/tmp_MMseqs2_output --search-type 2 --threads 8 -e 1e-10 --format-output query,qlen,target,tlen,alnlen,qstart,qend,tstart,tend,fident,nident,gapopen,mismatch,evalue,bits,qaln,taln ...
2025-08-18 21:14:43.171 | INFO     | dnaapler.utils.external_tools:run:54 - Done running mmseqs easy-search results/bsubtilis/circularization/rotated_input.fasta /home/pabloati/miniforge3/envs/pablo_course/lib/python3.12/site-packages/dnaapler/db/all_db results/bsubtilis/circularization/dnaapler_MMseqs2_output.txt results/bsubtilis/circularization/tmp_MMseqs2_output --search-type 2 --threads 8 -e 1e-10 --format-output query,qlen,target,tlen,alnlen,qstart,qend,tstart,tend,fident,nident,gapopen,mismatch,evalue,bits,qaln,taln
2025-08-18 21:14:43.241 | WARNING  | dnaapler.utils.processing:reorient_single_record_bulk:512 - The top MMseqs2 hit for the contig contig_2 did not begin with a valid start codon.
2025-08-18 21:14:43.241 | WARNING  | dnaapler.utils.processing:reorient_single_record_bulk:515 - Searching with pyrodigal for the CDS overlapping the most with the top MMseqs2 hit to reorient with.
2025-08-18 21:14:43.343 | INFO     | dnaapler.utils.util:end_dnaapler:173 - dnaapler has finished
2025-08-18 21:14:43.343 | INFO     | dnaapler.utils.util:end_dnaapler:174 - Elapsed time: 27.37 seconds