[2024-01-24 12:13:27,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,545] [INFO] DQC Reference Directory: /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference
[2024-01-24 12:13:28,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,962] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2a612ea-3bab-4e91-bcda-3745bf4a30c9/GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/cds.fna -a GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:42,519] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:42,519] [INFO] Task started: HMMsearch
[2024-01-24 12:13:42,519] [INFO] Running command: hmmsearch --tblout GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/reference_markers.hmm GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:42,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:42,824] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,845] [INFO] Query marker FASTA was written to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:42,846] [INFO] Task started: Blastn
[2024-01-24 12:13:42,846] [INFO] Running command: blastn -query GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/reference_markers.fasta -out GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:43,423] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:43,426] [INFO] Selected 17 target genomes.
[2024-01-24 12:13:43,427] [INFO] Target genome list was writen to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:43,433] [INFO] Task started: fastANI
[2024-01-24 12:13:43,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a612ea-3bab-4e91-bcda-3745bf4a30c9/GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna.gz --refList GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,944] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,951] [INFO] Found 3 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:13:55,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,952] [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
Porphyromonas cangingivalis	strain=ATCC 700135	GCA_900167355.1	36874	36874	type	True	100.0	770	773	95	conclusive
Porphyromonas cangingivalis	strain=NCTC12856	GCA_900638305.1	36874	36874	type	True	99.9961	772	773	95	conclusive
Porphyromonas cangingivalis	strain=JCM 15983	GCA_000614355.1	36874	36874	type	True	99.9263	749	773	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,954] [INFO] DFAST Taxonomy check result was written to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/checkm_data
[2024-01-24 12:13:55,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,986] [INFO] Task started: CheckM
[2024-01-24 12:13:55,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/checkm_input GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:41,045] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:41,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:41,069] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:41,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:41,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:41,070] [INFO] Task started: Blastn
[2024-01-24 12:14:41,070] [INFO] Running command: blastn -query GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd13d5e4d-37a8-45b3-9a74-39d2c1e5fc91/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:41,912] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:41,916] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:41,916] [INFO] Target genome list was writen to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:42,232] [INFO] Task started: fastANI
[2024-01-24 12:14:42,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a612ea-3bab-4e91-bcda-3745bf4a30c9/GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna.gz --refList GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:56,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:56,512] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:56,512] [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
GCF_900638305.1	s__Porphyromonas_A cangingivalis	99.9961	772	773	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas_A	95.0	98.92	98.01	0.94	0.87	6	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,514] [INFO] GTDB search result was written to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:56,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:56,518] [INFO] DFAST_QC result json was written to GCF_900167355.1_IMG-taxon_2585428082_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:56,519] [INFO] DFAST_QC completed!
[2024-01-24 12:14:56,519] [INFO] Total running time: 0h1m29s