[2024-01-24 12:46:56,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:56,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:56,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference
[2024-01-24 12:46:57,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:57,981] [INFO] Task started: Prodigal
[2024-01-24 12:46:57,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg348eb581-dacb-4175-9c7f-cb9e709ef9ea/GCF_009684715.1_ASM968471v1_genomic.fna.gz | prodigal -d GCF_009684715.1_ASM968471v1_genomic.fna/cds.fna -a GCF_009684715.1_ASM968471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:01,993] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:01,993] [INFO] Task started: HMMsearch
[2024-01-24 12:47:01,994] [INFO] Running command: hmmsearch --tblout GCF_009684715.1_ASM968471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/reference_markers.hmm GCF_009684715.1_ASM968471v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:02,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:02,257] [INFO] Found 6/6 markers.
[2024-01-24 12:47:02,284] [INFO] Query marker FASTA was written to GCF_009684715.1_ASM968471v1_genomic.fna/markers.fasta
[2024-01-24 12:47:02,284] [INFO] Task started: Blastn
[2024-01-24 12:47:02,285] [INFO] Running command: blastn -query GCF_009684715.1_ASM968471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/reference_markers.fasta -out GCF_009684715.1_ASM968471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:02,955] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:02,959] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:02,959] [INFO] Target genome list was writen to GCF_009684715.1_ASM968471v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:02,982] [INFO] Task started: fastANI
[2024-01-24 12:47:02,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg348eb581-dacb-4175-9c7f-cb9e709ef9ea/GCF_009684715.1_ASM968471v1_genomic.fna.gz --refList GCF_009684715.1_ASM968471v1_genomic.fna/target_genomes.txt --output GCF_009684715.1_ASM968471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:12,513] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:12,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:12,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:12,531] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:12,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:12,531] [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
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	100.0	671	673	95	conclusive
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	99.9835	656	673	95	conclusive
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	78.9894	209	673	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.9845	272	673	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.8836	271	673	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	78.8755	163	673	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.7689	143	673	95	below_threshold
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	78.682	140	673	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.5912	222	673	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	78.435	200	673	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.3376	151	673	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	78.2454	156	673	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.1657	217	673	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.1417	167	673	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	78.1352	134	673	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	78.0762	141	673	95	below_threshold
Nicoletella semolina	strain=DSM 16380	GCA_004345745.1	271160	271160	type	True	78.0675	146	673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:12,533] [INFO] DFAST Taxonomy check result was written to GCF_009684715.1_ASM968471v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:12,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:12,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:12,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/checkm_data
[2024-01-24 12:47:12,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:12,557] [INFO] Task started: CheckM
[2024-01-24 12:47:12,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009684715.1_ASM968471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009684715.1_ASM968471v1_genomic.fna/checkm_input GCF_009684715.1_ASM968471v1_genomic.fna/checkm_result
[2024-01-24 12:47:32,440] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:32,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:32,464] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:32,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:32,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009684715.1_ASM968471v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:32,465] [INFO] Task started: Blastn
[2024-01-24 12:47:32,465] [INFO] Running command: blastn -query GCF_009684715.1_ASM968471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5113806b-41de-4aa5-a18b-4890cf330f5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009684715.1_ASM968471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:33,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:33,536] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:33,536] [INFO] Target genome list was writen to GCF_009684715.1_ASM968471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:33,566] [INFO] Task started: fastANI
[2024-01-24 12:47:33,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg348eb581-dacb-4175-9c7f-cb9e709ef9ea/GCF_009684715.1_ASM968471v1_genomic.fna.gz --refList GCF_009684715.1_ASM968471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009684715.1_ASM968471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:42,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:42,744] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:42,745] [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_009684715.1	s__Otariodibacter oris	100.0	670	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_011455495.1	s__Frederiksenia canicola	79.3007	196	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013377195.1	s__Bisgaardia hudsonensis	79.1162	168	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.9928	186	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.9404	151	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009761395.1	s__Ursidibacter maritimus	78.8916	271	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_000521605.1	s__Mannheimia sp000521605	78.8914	163	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009761375.1	s__Ursidibacter arcticus	78.8481	262	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014541205.1	s__Mannheimia bovis	78.7866	161	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931275.1	s__Haemophilus_D sp900755445	78.7766	141	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_001038205.1	s__Muribacter muris	78.6028	115	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Muribacter	95.0	96.52	96.51	0.85	0.84	5	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	78.5818	220	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.5492	231	673	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_018343795.1	s__Phocoenobacter atlantica	78.4727	169	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002015085.1	s__Glaesserella parasuis	78.435	200	673	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	78.3877	235	673	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	78.3833	179	673	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_000238795.1	s__Haemophilus_A sputorum	78.3608	151	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	78.2156	128	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCF_000191405.1	s__Haemophilus_D parainfluenzae	78.119	135	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCF_000374285.1	s__Actinobacillus capsulatus	78.0903	170	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345745.1	s__Nicoletella semolina	78.0652	146	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Nicoletella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214375.1	s__Haemophilus_D sp905214375	77.4359	94	673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:42,746] [INFO] GTDB search result was written to GCF_009684715.1_ASM968471v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:42,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:42,751] [INFO] DFAST_QC result json was written to GCF_009684715.1_ASM968471v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:42,751] [INFO] DFAST_QC completed!
[2024-01-24 12:47:42,751] [INFO] Total running time: 0h0m46s