[2024-01-24 12:06:33,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,725] [INFO] DQC Reference Directory: /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference
[2024-01-24 12:06:34,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,931] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg31a8aa3a-9074-4c7c-96df-2e9d4b848652/GCF_002015085.1_ASM201508v1_genomic.fna.gz | prodigal -d GCF_002015085.1_ASM201508v1_genomic.fna/cds.fna -a GCF_002015085.1_ASM201508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:40,036] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:40,037] [INFO] Task started: HMMsearch
[2024-01-24 12:06:40,037] [INFO] Running command: hmmsearch --tblout GCF_002015085.1_ASM201508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/reference_markers.hmm GCF_002015085.1_ASM201508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:40,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:40,276] [INFO] Found 6/6 markers.
[2024-01-24 12:06:40,303] [INFO] Query marker FASTA was written to GCF_002015085.1_ASM201508v1_genomic.fna/markers.fasta
[2024-01-24 12:06:40,303] [INFO] Task started: Blastn
[2024-01-24 12:06:40,304] [INFO] Running command: blastn -query GCF_002015085.1_ASM201508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/reference_markers.fasta -out GCF_002015085.1_ASM201508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:40,994] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:40,998] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:40,998] [INFO] Target genome list was writen to GCF_002015085.1_ASM201508v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:41,025] [INFO] Task started: fastANI
[2024-01-24 12:06:41,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a8aa3a-9074-4c7c-96df-2e9d4b848652/GCF_002015085.1_ASM201508v1_genomic.fna.gz --refList GCF_002015085.1_ASM201508v1_genomic.fna/target_genomes.txt --output GCF_002015085.1_ASM201508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:50,090] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:50,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:50,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:50,102] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:50,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:50,102] [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
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	100.0	726	730	95	conclusive
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	99.9882	730	730	95	conclusive
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	79.3556	277	730	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	79.3475	279	730	95	below_threshold
Frederiksenia canicola	strain=HPA 21	GCA_011455495.1	123824	123824	type	True	79.3153	254	730	95	below_threshold
Frederiksenia canicola	strain=DSM 25797	GCA_003814575.1	123824	123824	type	True	79.3083	255	730	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	79.0314	224	730	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	78.815	229	730	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	78.7667	234	730	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	78.6758	204	730	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	78.5531	194	730	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.4288	203	730	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.2911	228	730	95	below_threshold
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	78.2288	121	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,104] [INFO] DFAST Taxonomy check result was written to GCF_002015085.1_ASM201508v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:50,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:50,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:50,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/checkm_data
[2024-01-24 12:06:50,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:50,130] [INFO] Task started: CheckM
[2024-01-24 12:06:50,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002015085.1_ASM201508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002015085.1_ASM201508v1_genomic.fna/checkm_input GCF_002015085.1_ASM201508v1_genomic.fna/checkm_result
[2024-01-24 12:07:11,849] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:11,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:11,871] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:11,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:11,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002015085.1_ASM201508v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:11,872] [INFO] Task started: Blastn
[2024-01-24 12:07:11,872] [INFO] Running command: blastn -query GCF_002015085.1_ASM201508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d61d95-b5e2-4cf9-9bee-9b5682e3d614/dqc_reference/reference_markers_gtdb.fasta -out GCF_002015085.1_ASM201508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:12,918] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:12,924] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:12,924] [INFO] Target genome list was writen to GCF_002015085.1_ASM201508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:12,936] [INFO] Task started: fastANI
[2024-01-24 12:07:12,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a8aa3a-9074-4c7c-96df-2e9d4b848652/GCF_002015085.1_ASM201508v1_genomic.fna.gz --refList GCF_002015085.1_ASM201508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002015085.1_ASM201508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:18,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:18,592] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:18,592] [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_002015085.1	s__Glaesserella parasuis	100.0	726	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	conclusive
GCF_004519515.1	s__Glaesserella indolica_A	88.924	458	730	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	88.7347	447	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000175195.1	s__Actinobacillus_A minor	83.3368	280	730	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_003260095.1	s__Glaesserella australis	82.7132	417	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002002485.1	s__GCF-002002485 sp002002485	79.3964	289	730	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_009761395.1	s__Ursidibacter maritimus	79.373	275	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_009761375.1	s__Ursidibacter arcticus	79.3461	284	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346205.1	s__Bibersteinia trehalosi	78.991	226	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bibersteinia	95.0	98.14	97.86	0.95	0.93	7	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.8673	225	730	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	78.775	233	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_013377255.1	s__Mannheimia granulomatis	78.6385	226	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,595] [INFO] GTDB search result was written to GCF_002015085.1_ASM201508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:18,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:18,599] [INFO] DFAST_QC result json was written to GCF_002015085.1_ASM201508v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:18,599] [INFO] DFAST_QC completed!
[2024-01-24 12:07:18,599] [INFO] Total running time: 0h0m45s