[2024-01-24 12:14:33,702] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference
[2024-01-24 12:14:35,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,035] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c3ba42d-4391-4049-b730-40ec60312e3c/GCF_004346205.1_ASM434620v1_genomic.fna.gz | prodigal -d GCF_004346205.1_ASM434620v1_genomic.fna/cds.fna -a GCF_004346205.1_ASM434620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:40,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:40,579] [INFO] Task started: HMMsearch
[2024-01-24 12:14:40,579] [INFO] Running command: hmmsearch --tblout GCF_004346205.1_ASM434620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/reference_markers.hmm GCF_004346205.1_ASM434620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:40,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:40,870] [INFO] Found 6/6 markers.
[2024-01-24 12:14:40,904] [INFO] Query marker FASTA was written to GCF_004346205.1_ASM434620v1_genomic.fna/markers.fasta
[2024-01-24 12:14:40,905] [INFO] Task started: Blastn
[2024-01-24 12:14:40,905] [INFO] Running command: blastn -query GCF_004346205.1_ASM434620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/reference_markers.fasta -out GCF_004346205.1_ASM434620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:41,588] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:41,593] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:41,594] [INFO] Target genome list was writen to GCF_004346205.1_ASM434620v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:41,607] [INFO] Task started: fastANI
[2024-01-24 12:14:41,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3ba42d-4391-4049-b730-40ec60312e3c/GCF_004346205.1_ASM434620v1_genomic.fna.gz --refList GCF_004346205.1_ASM434620v1_genomic.fna/target_genomes.txt --output GCF_004346205.1_ASM434620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:53,096] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:53,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:53,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:53,113] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:53,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:53,114] [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
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	100.0	748	749	95	conclusive
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	80.8623	237	749	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	80.8617	243	749	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	79.0012	233	749	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	78.7475	166	749	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	78.7475	166	749	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.578	205	749	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.5679	205	749	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	78.562	175	749	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.5175	156	749	95	below_threshold
Frederiksenia canicola	strain=HPA 21	GCA_011455495.1	123824	123824	type	True	78.5172	212	749	95	below_threshold
Frederiksenia canicola	strain=DSM 25797	GCA_003814575.1	123824	123824	type	True	78.4969	213	749	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	78.3598	176	749	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	78.3155	207	749	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.2727	200	749	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	77.9939	171	749	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	77.9832	145	749	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	77.9067	174	749	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	77.8495	138	749	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	77.6959	110	749	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	77.6506	105	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,117] [INFO] DFAST Taxonomy check result was written to GCF_004346205.1_ASM434620v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:53,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:53,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:53,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/checkm_data
[2024-01-24 12:14:53,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:53,148] [INFO] Task started: CheckM
[2024-01-24 12:14:53,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346205.1_ASM434620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346205.1_ASM434620v1_genomic.fna/checkm_input GCF_004346205.1_ASM434620v1_genomic.fna/checkm_result
[2024-01-24 12:15:16,584] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:16,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:16,604] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:16,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:16,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346205.1_ASM434620v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:16,605] [INFO] Task started: Blastn
[2024-01-24 12:15:16,605] [INFO] Running command: blastn -query GCF_004346205.1_ASM434620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db8f449-980e-492d-ac4a-45f91a7c3ae6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346205.1_ASM434620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:17,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:17,839] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:17,840] [INFO] Target genome list was writen to GCF_004346205.1_ASM434620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:17,857] [INFO] Task started: fastANI
[2024-01-24 12:15:17,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3ba42d-4391-4049-b730-40ec60312e3c/GCF_004346205.1_ASM434620v1_genomic.fna.gz --refList GCF_004346205.1_ASM434620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346205.1_ASM434620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:27,605] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:27,623] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:27,623] [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_004346205.1	s__Bibersteinia trehalosi	100.0	748	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bibersteinia	95.0	98.14	97.86	0.95	0.93	7	conclusive
GCF_004519515.1	s__Glaesserella indolica_A	78.8479	256	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901764975.1	s__Glaesserella indolica	78.7591	256	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260095.1	s__Glaesserella australis	78.7174	248	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.6369	204	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_009761395.1	s__Ursidibacter maritimus	78.5957	203	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_900444945.1	s__Actinobacillus lignieresii	78.5828	174	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.57	209	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455495.1	s__Frederiksenia canicola	78.5172	212	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	78.4651	159	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	78.3908	175	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCF_003096995.1	s__Basfia_A langaaensis	78.3445	118	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	78.335	198	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901687125.1	s__Actinobacillus vicugnae	78.3347	217	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238795.1	s__Haemophilus_A sputorum	78.2641	170	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.1837	232	749	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_009761375.1	s__Ursidibacter arcticus	78.166	216	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454895.1	s__Phocoenobacter uteri	78.1541	119	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.8248	115	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018373095.1	s__Haemophilus_A parahaemolyticus_A	77.7673	143	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262245.1	s__Basfia bettyae	77.6802	104	749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,625] [INFO] GTDB search result was written to GCF_004346205.1_ASM434620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:27,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:27,631] [INFO] DFAST_QC result json was written to GCF_004346205.1_ASM434620v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:27,631] [INFO] DFAST_QC completed!
[2024-01-24 12:15:27,631] [INFO] Total running time: 0h0m54s