[2024-01-24 11:35:22,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg000e61f4-0113-4abe-a062-fff21e8f3682/GCF_013377295.1_ASM1337729v1_genomic.fna.gz | prodigal -d GCF_013377295.1_ASM1337729v1_genomic.fna/cds.fna -a GCF_013377295.1_ASM1337729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:30,684] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:30,685] [INFO] Task started: HMMsearch
[2024-01-24 11:35:30,685] [INFO] Running command: hmmsearch --tblout GCF_013377295.1_ASM1337729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/reference_markers.hmm GCF_013377295.1_ASM1337729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:30,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:30,971] [INFO] Found 6/6 markers.
[2024-01-24 11:35:30,996] [INFO] Query marker FASTA was written to GCF_013377295.1_ASM1337729v1_genomic.fna/markers.fasta
[2024-01-24 11:35:30,997] [INFO] Task started: Blastn
[2024-01-24 11:35:30,997] [INFO] Running command: blastn -query GCF_013377295.1_ASM1337729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/reference_markers.fasta -out GCF_013377295.1_ASM1337729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:32,961] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:32,965] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:32,966] [INFO] Target genome list was writen to GCF_013377295.1_ASM1337729v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,038] [INFO] Task started: fastANI
[2024-01-24 11:35:33,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg000e61f4-0113-4abe-a062-fff21e8f3682/GCF_013377295.1_ASM1337729v1_genomic.fna.gz --refList GCF_013377295.1_ASM1337729v1_genomic.fna/target_genomes.txt --output GCF_013377295.1_ASM1337729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:42,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:42,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:42,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:42,229] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:42,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:42,229] [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
Pasteurella skyensis	strain=95A1	GCA_013377295.1	97481	97481	type	True	100.0	747	748	95	conclusive
Pasteurella skyensis	strain=DSM 24204	GCA_900109845.1	97481	97481	type	True	99.8993	693	748	95	conclusive
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	78.713	133	748	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	78.5367	125	748	95	below_threshold
Bisgaardia hudsonensis	strain=M327/99/2	GCA_013377195.1	109472	109472	type	True	78.4862	134	748	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	78.3978	130	748	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	78.282	151	748	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	78.1793	153	748	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	78.1597	124	748	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.1345	167	748	95	below_threshold
Cricetibacter osteomyelitidis	strain=DSM 28404	GCA_004340985.1	1521931	1521931	type	True	78.0076	76	748	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	77.8317	98	748	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	77.8002	137	748	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	77.7449	128	748	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	77.5245	155	748	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	77.5181	119	748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:42,231] [INFO] DFAST Taxonomy check result was written to GCF_013377295.1_ASM1337729v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:42,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:42,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:42,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/checkm_data
[2024-01-24 11:35:42,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:42,259] [INFO] Task started: CheckM
[2024-01-24 11:35:42,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377295.1_ASM1337729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377295.1_ASM1337729v1_genomic.fna/checkm_input GCF_013377295.1_ASM1337729v1_genomic.fna/checkm_result
[2024-01-24 11:36:02,877] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:02,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:02,901] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:02,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:02,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377295.1_ASM1337729v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:02,902] [INFO] Task started: Blastn
[2024-01-24 11:36:02,902] [INFO] Running command: blastn -query GCF_013377295.1_ASM1337729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec69a28a-1cca-4857-adb9-089338a8f898/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377295.1_ASM1337729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:03,805] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:03,808] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:03,808] [INFO] Target genome list was writen to GCF_013377295.1_ASM1337729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:03,823] [INFO] Task started: fastANI
[2024-01-24 11:36:03,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg000e61f4-0113-4abe-a062-fff21e8f3682/GCF_013377295.1_ASM1337729v1_genomic.fna.gz --refList GCF_013377295.1_ASM1337729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377295.1_ASM1337729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:11,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:11,225] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:11,225] [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_013377295.1	s__Phocoenobacter skyensis	100.0	747	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_018343795.1	s__Phocoenobacter atlantica	88.0436	479	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900454895.1	s__Phocoenobacter uteri	82.3944	373	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	78.7406	126	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_004519515.1	s__Glaesserella indolica_A	78.7405	146	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521605.1	s__Mannheimia sp000521605	78.7075	127	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	78.5515	115	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_013377195.1	s__Bisgaardia hudsonensis	78.4845	136	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900636745.1	s__Actinobacillus equuli	78.4804	129	748	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	78.2193	122	748	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_004802395.1	s__Haemophilus influenzae_E	78.217	115	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.8621	97.44	97.09	0.92	0.89	88	-
GCF_009761395.1	s__Ursidibacter maritimus	78.2111	151	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	78.2049	164	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_901764975.1	s__Glaesserella indolica	78.0671	133	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004340985.1	s__Cricetibacter osteomyelitidis	78.0596	76	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384255.1	s__Haemophilus seminalis	77.8333	98	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	96.02	95.40	0.91	0.84	26	-
GCF_002015085.1	s__Glaesserella parasuis	77.7754	138	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:11,227] [INFO] GTDB search result was written to GCF_013377295.1_ASM1337729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:11,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:11,236] [INFO] DFAST_QC result json was written to GCF_013377295.1_ASM1337729v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:11,237] [INFO] DFAST_QC completed!
[2024-01-24 11:36:11,238] [INFO] Total running time: 0h0m49s