[2024-01-24 12:15:04,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference
[2024-01-24 12:15:05,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,361] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f9e12bc-9a9e-4ff5-820d-f9de80bdabbb/GCF_001038205.1_ASM103820v1_genomic.fna.gz | prodigal -d GCF_001038205.1_ASM103820v1_genomic.fna/cds.fna -a GCF_001038205.1_ASM103820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:10,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:10,941] [INFO] Task started: HMMsearch
[2024-01-24 12:15:10,941] [INFO] Running command: hmmsearch --tblout GCF_001038205.1_ASM103820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/reference_markers.hmm GCF_001038205.1_ASM103820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:11,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:11,153] [INFO] Found 6/6 markers.
[2024-01-24 12:15:11,181] [INFO] Query marker FASTA was written to GCF_001038205.1_ASM103820v1_genomic.fna/markers.fasta
[2024-01-24 12:15:11,182] [INFO] Task started: Blastn
[2024-01-24 12:15:11,182] [INFO] Running command: blastn -query GCF_001038205.1_ASM103820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/reference_markers.fasta -out GCF_001038205.1_ASM103820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:11,825] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:11,829] [INFO] Selected 28 target genomes.
[2024-01-24 12:15:11,829] [INFO] Target genome list was writen to GCF_001038205.1_ASM103820v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:11,838] [INFO] Task started: fastANI
[2024-01-24 12:15:11,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9e12bc-9a9e-4ff5-820d-f9de80bdabbb/GCF_001038205.1_ASM103820v1_genomic.fna.gz --refList GCF_001038205.1_ASM103820v1_genomic.fna/target_genomes.txt --output GCF_001038205.1_ASM103820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:26,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:26,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:26,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:26,527] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:26,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:26,528] [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
Muribacter muris	strain=Ackerman80-443D	GCA_001038205.1	67855	67855	type	True	100.0	750	754	95	conclusive
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	78.6954	228	754	95	below_threshold
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	78.6946	109	754	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	78.6838	225	754	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	78.651	109	754	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.5645	171	754	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.5247	131	754	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.43	132	754	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.4062	171	754	95	below_threshold
Haemophilus paracuniculus	strain=CCUG 43573	GCA_002015115.1	734	734	type	True	78.312	248	754	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	78.223	197	754	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	78.2204	196	754	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	78.1742	167	754	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	77.6567	184	754	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	77.3299	116	754	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	77.1322	115	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,530] [INFO] DFAST Taxonomy check result was written to GCF_001038205.1_ASM103820v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:26,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:26,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:26,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/checkm_data
[2024-01-24 12:15:26,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:26,559] [INFO] Task started: CheckM
[2024-01-24 12:15:26,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001038205.1_ASM103820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001038205.1_ASM103820v1_genomic.fna/checkm_input GCF_001038205.1_ASM103820v1_genomic.fna/checkm_result
[2024-01-24 12:15:49,208] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001038205.1_ASM103820v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,229] [INFO] Task started: Blastn
[2024-01-24 12:15:49,229] [INFO] Running command: blastn -query GCF_001038205.1_ASM103820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7c67e0-6dc3-469c-bc2d-12f82f4958af/dqc_reference/reference_markers_gtdb.fasta -out GCF_001038205.1_ASM103820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:50,034] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:50,037] [INFO] Selected 24 target genomes.
[2024-01-24 12:15:50,037] [INFO] Target genome list was writen to GCF_001038205.1_ASM103820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:50,053] [INFO] Task started: fastANI
[2024-01-24 12:15:50,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9e12bc-9a9e-4ff5-820d-f9de80bdabbb/GCF_001038205.1_ASM103820v1_genomic.fna.gz --refList GCF_001038205.1_ASM103820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001038205.1_ASM103820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:59,686] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:59,703] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:59,704] [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_001038205.1	s__Muribacter muris	100.0	750	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Muribacter	95.0	96.52	96.51	0.85	0.84	5	conclusive
GCF_011455495.1	s__Frederiksenia canicola	78.9371	209	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001998825.1	s__Rodentibacter mrazii	78.7356	106	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_009684715.1	s__Otariodibacter oris	78.733	108	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002015085.1	s__Glaesserella parasuis	78.6838	225	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	-
GCF_901764975.1	s__Glaesserella indolica	78.5816	233	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.5451	234	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009761375.1	s__Ursidibacter arcticus	78.5256	177	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	78.43	132	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009761395.1	s__Ursidibacter maritimus	78.3828	172	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_003260095.1	s__Glaesserella australis	78.3406	241	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002015115.1	s__Haemophilus_E paracuniculus	78.3059	249	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342115.1	s__Mannheimia haemolytica	78.2019	197	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_013377235.1	s__Mannheimia varigena	78.182	166	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_002263215.1	s__Actinobacillus_B seminis	78.0155	97	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	99.95	99.95	1.00	1.00	2	-
GCF_013377255.1	s__Mannheimia granulomatis	77.9774	163	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_900636745.1	s__Actinobacillus equuli	77.79	188	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCA_012221805.1	s__RH1A sp012221805	77.6414	131	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__RH1A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	77.64	185	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202395.1	s__Histophilus somni	77.5089	74	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCF_900176075.1	s__Chelonobacter testudinis	77.1556	114	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,705] [INFO] GTDB search result was written to GCF_001038205.1_ASM103820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:59,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:59,710] [INFO] DFAST_QC result json was written to GCF_001038205.1_ASM103820v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:59,710] [INFO] DFAST_QC completed!
[2024-01-24 12:15:59,710] [INFO] Total running time: 0h0m56s