[2023-06-07 20:40:02,328] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:02,336] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:02,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference
[2023-06-07 20:40:03,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:03,784] [INFO] Task started: Prodigal
[2023-06-07 20:40:03,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc2bc54b-ec3e-4694-a662-c9f127682b39/GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna.gz | prodigal -d GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/cds.fna -a GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:07,124] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:07,124] [INFO] Task started: HMMsearch
[2023-06-07 20:40:07,124] [INFO] Running command: hmmsearch --tblout GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/reference_markers.hmm GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:07,402] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:07,403] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcc2bc54b-ec3e-4694-a662-c9f127682b39/GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna.gz]
[2023-06-07 20:40:07,422] [INFO] Query marker FASTA was written to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/markers.fasta
[2023-06-07 20:40:07,422] [INFO] Task started: Blastn
[2023-06-07 20:40:07,422] [INFO] Running command: blastn -query GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/reference_markers.fasta -out GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:08,159] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:08,166] [INFO] Selected 29 target genomes.
[2023-06-07 20:40:08,166] [INFO] Target genome list was writen to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/target_genomes.txt
[2023-06-07 20:40:08,198] [INFO] Task started: fastANI
[2023-06-07 20:40:08,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2bc54b-ec3e-4694-a662-c9f127682b39/GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna.gz --refList GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/target_genomes.txt --output GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:30,018] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:30,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:30,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:30,024] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:30,025] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:40:30,025] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-07 20:40:30,027] [INFO] DFAST Taxonomy check result was written to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/tc_result.tsv
[2023-06-07 20:40:30,028] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:30,029] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:30,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/checkm_data
[2023-06-07 20:40:30,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:30,055] [INFO] Task started: CheckM
[2023-06-07 20:40:30,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/checkm_input GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/checkm_result
[2023-06-07 20:40:47,562] [INFO] Task succeeded: CheckM
[2023-06-07 20:40:47,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.73%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:40:47,588] [INFO] ===== Completeness check finished =====
[2023-06-07 20:40:47,588] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:40:47,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/markers.fasta)
[2023-06-07 20:40:47,589] [INFO] Task started: Blastn
[2023-06-07 20:40:47,589] [INFO] Running command: blastn -query GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf43798d-f75c-4435-9cff-e0e23f9c6962/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:48,593] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:48,597] [INFO] Selected 13 target genomes.
[2023-06-07 20:40:48,598] [INFO] Target genome list was writen to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:40:48,603] [INFO] Task started: fastANI
[2023-06-07 20:40:48,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2bc54b-ec3e-4694-a662-c9f127682b39/GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna.gz --refList GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/target_genomes_gtdb.txt --output GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:40:52,672] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:52,684] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:40:52,685] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902778985.1	s__UBA1740 sp902778985	100.0	417	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	97.18	97.18	0.82	0.82	2	conclusive
GCA_902779285.1	s__UBA1740 sp902779285	86.7664	350	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	97.26	97.26	0.85	0.85	2	-
GCA_017960705.1	s__UBA1740 sp017960705	86.2896	309	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961575.1	s__UBA1740 sp017961575	84.7421	338	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796505.1	s__UBA1740 sp902796505	76.8101	60	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556685.1	s__UBA1740 sp017556685	76.69	67	421	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1740	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:40:52,687] [INFO] GTDB search result was written to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/result_gtdb.tsv
[2023-06-07 20:40:52,688] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:40:52,691] [INFO] DFAST_QC result json was written to GCA_902778985.1_Rumen_uncultured_genome_RUG12422_genomic.fna/dqc_result.json
[2023-06-07 20:40:52,691] [INFO] DFAST_QC completed!
[2023-06-07 20:40:52,691] [INFO] Total running time: 0h0m50s