[2024-01-25 18:44:35,778] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,780] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference
[2024-01-25 18:44:36,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,897] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3218854-ed12-4c48-b526-cefb6fb8dfe3/GCF_009761395.1_ASM976139v1_genomic.fna.gz | prodigal -d GCF_009761395.1_ASM976139v1_genomic.fna/cds.fna -a GCF_009761395.1_ASM976139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:40,416] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:40,416] [INFO] Task started: HMMsearch
[2024-01-25 18:44:40,416] [INFO] Running command: hmmsearch --tblout GCF_009761395.1_ASM976139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/reference_markers.hmm GCF_009761395.1_ASM976139v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:40,616] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:40,617] [INFO] Found 6/6 markers.
[2024-01-25 18:44:40,636] [INFO] Query marker FASTA was written to GCF_009761395.1_ASM976139v1_genomic.fna/markers.fasta
[2024-01-25 18:44:40,636] [INFO] Task started: Blastn
[2024-01-25 18:44:40,636] [INFO] Running command: blastn -query GCF_009761395.1_ASM976139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/reference_markers.fasta -out GCF_009761395.1_ASM976139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:41,223] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:41,226] [INFO] Selected 25 target genomes.
[2024-01-25 18:44:41,226] [INFO] Target genome list was writen to GCF_009761395.1_ASM976139v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:41,259] [INFO] Task started: fastANI
[2024-01-25 18:44:41,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3218854-ed12-4c48-b526-cefb6fb8dfe3/GCF_009761395.1_ASM976139v1_genomic.fna.gz --refList GCF_009761395.1_ASM976139v1_genomic.fna/target_genomes.txt --output GCF_009761395.1_ASM976139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:51,953] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:51,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:51,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:51,964] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:51,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:51,965] [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
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	100.0	641	643	95	conclusive
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	99.9981	643	643	95	conclusive
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	79.094	303	643	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	79.0882	302	643	95	below_threshold
Frederiksenia canicola	strain=DSM 25797	GCA_003814575.1	123824	123824	type	True	78.812	275	643	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	78.7919	269	643	95	below_threshold
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	78.7857	270	643	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.7193	266	643	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.6713	273	643	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	78.448	221	643	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	78.441	189	643	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	78.2144	213	643	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.1852	196	643	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	77.9822	143	643	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	77.9656	142	643	95	below_threshold
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	77.9283	144	643	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	77.9018	143	643	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	77.8009	185	643	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	77.7472	188	643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:51,967] [INFO] DFAST Taxonomy check result was written to GCF_009761395.1_ASM976139v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:51,967] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:51,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:51,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/checkm_data
[2024-01-25 18:44:51,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:51,990] [INFO] Task started: CheckM
[2024-01-25 18:44:51,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009761395.1_ASM976139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009761395.1_ASM976139v1_genomic.fna/checkm_input GCF_009761395.1_ASM976139v1_genomic.fna/checkm_result
[2024-01-25 18:45:08,740] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:08,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:08,755] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:08,755] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:08,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009761395.1_ASM976139v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:08,755] [INFO] Task started: Blastn
[2024-01-25 18:45:08,755] [INFO] Running command: blastn -query GCF_009761395.1_ASM976139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00943af-f215-466f-be4c-37be71030a23/dqc_reference/reference_markers_gtdb.fasta -out GCF_009761395.1_ASM976139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:09,562] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:09,565] [INFO] Selected 22 target genomes.
[2024-01-25 18:45:09,565] [INFO] Target genome list was writen to GCF_009761395.1_ASM976139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:09,597] [INFO] Task started: fastANI
[2024-01-25 18:45:09,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3218854-ed12-4c48-b526-cefb6fb8dfe3/GCF_009761395.1_ASM976139v1_genomic.fna.gz --refList GCF_009761395.1_ASM976139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009761395.1_ASM976139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:18,940] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:18,953] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:18,954] [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_009761395.1	s__Ursidibacter maritimus	100.0	641	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	conclusive
GCF_009761375.1	s__Ursidibacter arcticus	91.7157	481	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260095.1	s__Glaesserella australis	79.2667	288	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002015085.1	s__Glaesserella parasuis	79.068	303	643	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	79.018	315	643	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	78.9659	213	643	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_011455495.1	s__Frederiksenia canicola	78.9304	272	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009684715.1	s__Otariodibacter oris	78.8182	268	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.6871	255	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	78.6713	273	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.5397	195	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636745.1	s__Actinobacillus equuli	78.5048	196	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000175195.1	s__Actinobacillus_A minor	78.448	221	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	78.441	189	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_901687125.1	s__Actinobacillus vicugnae	78.3849	223	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004802395.1	s__Haemophilus influenzae_E	78.2361	129	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.8621	97.44	97.09	0.92	0.89	88	-
GCF_000238795.1	s__Haemophilus_A sputorum	78.1364	200	643	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_905215245.1	s__Haemophilus_D sp905215245	78.0807	109	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	77.7671	90	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.6618	155	643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:18,956] [INFO] GTDB search result was written to GCF_009761395.1_ASM976139v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:18,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:18,965] [INFO] DFAST_QC result json was written to GCF_009761395.1_ASM976139v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:18,965] [INFO] DFAST_QC completed!
[2024-01-25 18:45:18,965] [INFO] Total running time: 0h0m43s