[2024-01-24 14:39:59,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:59,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:59,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference
[2024-01-24 14:40:00,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:00,735] [INFO] Task started: Prodigal
[2024-01-24 14:40:00,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg77b651d7-a5ed-465e-9016-af54fdecbe50/GCF_003843855.1_ASM384385v1_genomic.fna.gz | prodigal -d GCF_003843855.1_ASM384385v1_genomic.fna/cds.fna -a GCF_003843855.1_ASM384385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:04,533] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:04,534] [INFO] Task started: HMMsearch
[2024-01-24 14:40:04,534] [INFO] Running command: hmmsearch --tblout GCF_003843855.1_ASM384385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/reference_markers.hmm GCF_003843855.1_ASM384385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:04,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:04,852] [INFO] Found 6/6 markers.
[2024-01-24 14:40:04,877] [INFO] Query marker FASTA was written to GCF_003843855.1_ASM384385v1_genomic.fna/markers.fasta
[2024-01-24 14:40:04,878] [INFO] Task started: Blastn
[2024-01-24 14:40:04,878] [INFO] Running command: blastn -query GCF_003843855.1_ASM384385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/reference_markers.fasta -out GCF_003843855.1_ASM384385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:05,638] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:05,641] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:05,642] [INFO] Target genome list was writen to GCF_003843855.1_ASM384385v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:05,651] [INFO] Task started: fastANI
[2024-01-24 14:40:05,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b651d7-a5ed-465e-9016-af54fdecbe50/GCF_003843855.1_ASM384385v1_genomic.fna.gz --refList GCF_003843855.1_ASM384385v1_genomic.fna/target_genomes.txt --output GCF_003843855.1_ASM384385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,264] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:13,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,265] [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
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	100.0	586	586	95	conclusive
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	99.9973	585	586	95	conclusive
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.9954	261	586	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.9626	268	586	95	below_threshold
Frederiksenia canicola	strain=HPA 21	GCA_011455495.1	123824	123824	type	True	78.6991	216	586	95	below_threshold
Frederiksenia canicola	strain=DSM 25797	GCA_003814575.1	123824	123824	type	True	78.6302	222	586	95	below_threshold
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	78.5467	205	586	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	78.481	204	586	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	78.2969	211	586	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	78.2091	126	586	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	77.9891	120	586	95	below_threshold
Pasteurella dagmatis	strain=ATCC 43325	GCA_000163475.1	754	754	type	True	77.9698	116	586	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	77.9688	117	586	95	below_threshold
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	77.4844	91	586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,267] [INFO] DFAST Taxonomy check result was written to GCF_003843855.1_ASM384385v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/checkm_data
[2024-01-24 14:40:13,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,289] [INFO] Task started: CheckM
[2024-01-24 14:40:13,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003843855.1_ASM384385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003843855.1_ASM384385v1_genomic.fna/checkm_input GCF_003843855.1_ASM384385v1_genomic.fna/checkm_result
[2024-01-24 14:40:32,600] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:32,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:32,619] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:32,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:32,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003843855.1_ASM384385v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:32,621] [INFO] Task started: Blastn
[2024-01-24 14:40:32,621] [INFO] Running command: blastn -query GCF_003843855.1_ASM384385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967cc0c2-c1b9-4b92-a2e1-d8368387d5d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003843855.1_ASM384385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:33,737] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:33,740] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:33,740] [INFO] Target genome list was writen to GCF_003843855.1_ASM384385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:33,752] [INFO] Task started: fastANI
[2024-01-24 14:40:33,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b651d7-a5ed-465e-9016-af54fdecbe50/GCF_003843855.1_ASM384385v1_genomic.fna.gz --refList GCF_003843855.1_ASM384385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003843855.1_ASM384385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:40,953] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:40,968] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:40,968] [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_013377275.1	s__Vespertiliibacter pulmonis	99.9973	585	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009761395.1	s__Ursidibacter maritimus	79.0031	260	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_009761375.1	s__Ursidibacter arcticus	78.765	259	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455495.1	s__Frederiksenia canicola	78.6991	216	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.5703	200	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015085.1	s__Glaesserella parasuis	78.481	204	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	-
GCF_004519515.1	s__Glaesserella indolica_A	78.345	221	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260095.1	s__Glaesserella australis	78.305	204	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900636745.1	s__Actinobacillus equuli	78.2697	124	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_009684715.1	s__Otariodibacter oris	78.245	212	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	78.2091	126	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.208	194	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.1443	146	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901687125.1	s__Actinobacillus vicugnae	78.0276	169	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900444945.1	s__Actinobacillus lignieresii	77.9891	120	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_900186835.1	s__Pasteurella dagmatis	77.9426	118	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.4569	141	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:40,972] [INFO] GTDB search result was written to GCF_003843855.1_ASM384385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:40,973] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:40,980] [INFO] DFAST_QC result json was written to GCF_003843855.1_ASM384385v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:40,980] [INFO] DFAST_QC completed!
[2024-01-24 14:40:40,980] [INFO] Total running time: 0h0m42s