[2024-01-24 13:01:08,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:08,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:08,998] [INFO] DQC Reference Directory: /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference
[2024-01-24 13:01:10,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:10,177] [INFO] Task started: Prodigal
[2024-01-24 13:01:10,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ba6920c-f6c9-43a4-9e8f-1a0656cb3f3d/GCF_000067205.1_ASM6720v1_genomic.fna.gz | prodigal -d GCF_000067205.1_ASM6720v1_genomic.fna/cds.fna -a GCF_000067205.1_ASM6720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:27,308] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:27,308] [INFO] Task started: HMMsearch
[2024-01-24 13:01:27,308] [INFO] Running command: hmmsearch --tblout GCF_000067205.1_ASM6720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/reference_markers.hmm GCF_000067205.1_ASM6720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:27,627] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:27,629] [INFO] Found 6/6 markers.
[2024-01-24 13:01:27,672] [INFO] Query marker FASTA was written to GCF_000067205.1_ASM6720v1_genomic.fna/markers.fasta
[2024-01-24 13:01:27,672] [INFO] Task started: Blastn
[2024-01-24 13:01:27,673] [INFO] Running command: blastn -query GCF_000067205.1_ASM6720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/reference_markers.fasta -out GCF_000067205.1_ASM6720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:28,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:28,728] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:28,728] [INFO] Target genome list was writen to GCF_000067205.1_ASM6720v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:28,762] [INFO] Task started: fastANI
[2024-01-24 13:01:28,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ba6920c-f6c9-43a4-9e8f-1a0656cb3f3d/GCF_000067205.1_ASM6720v1_genomic.fna.gz --refList GCF_000067205.1_ASM6720v1_genomic.fna/target_genomes.txt --output GCF_000067205.1_ASM6720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:50,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:50,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:50,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:50,213] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:50,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:50,213] [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
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	82.7795	963	1762	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	82.7477	966	1762	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	82.7368	957	1762	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	82.7129	916	1762	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	82.6844	951	1762	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.6793	792	1762	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	82.6492	798	1762	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	82.5986	872	1762	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	82.596	866	1762	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_177	GCA_001525545.2	519	519	suspected-type	True	82.5945	885	1762	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	82.5628	876	1762	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	82.5555	821	1762	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	82.4976	834	1762	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	82.3702	922	1762	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	82.3108	898	1762	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	81.9446	909	1762	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	81.3961	870	1762	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.7305	395	1762	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.4033	390	1762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:50,215] [INFO] DFAST Taxonomy check result was written to GCF_000067205.1_ASM6720v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:50,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:50,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:50,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/checkm_data
[2024-01-24 13:01:50,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:50,265] [INFO] Task started: CheckM
[2024-01-24 13:01:50,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000067205.1_ASM6720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000067205.1_ASM6720v1_genomic.fna/checkm_input GCF_000067205.1_ASM6720v1_genomic.fna/checkm_result
[2024-01-24 13:02:39,324] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:39,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:39,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:39,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:39,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000067205.1_ASM6720v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:39,350] [INFO] Task started: Blastn
[2024-01-24 13:02:39,350] [INFO] Running command: blastn -query GCF_000067205.1_ASM6720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6971748-84c1-4ef3-a7dd-9ef4b1034a32/dqc_reference/reference_markers_gtdb.fasta -out GCF_000067205.1_ASM6720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:41,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:41,399] [INFO] Selected 7 target genomes.
[2024-01-24 13:02:41,400] [INFO] Target genome list was writen to GCF_000067205.1_ASM6720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:41,405] [INFO] Task started: fastANI
[2024-01-24 13:02:41,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ba6920c-f6c9-43a4-9e8f-1a0656cb3f3d/GCF_000067205.1_ASM6720v1_genomic.fna.gz --refList GCF_000067205.1_ASM6720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000067205.1_ASM6720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:51,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:51,554] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:51,554] [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_000067205.1	s__Bordetella_A petrii	100.0	1760	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017356245.1	s__Bordetella_A petrii_D	90.4297	1288	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745595.1	s__Bordetella_A petrii_C	87.8551	1201	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218885.1	s__Bordetella_A sp019218885	86.4544	1191	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	85.6236	1139	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_002261265.1	s__Bordetella_A sp002261265	83.9359	1015	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.22	99.22	0.95	0.94	3	-
GCF_002119665.1	s__Bordetella_B sp002119665	82.201	869	1762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:51,556] [INFO] GTDB search result was written to GCF_000067205.1_ASM6720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:51,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:51,562] [INFO] DFAST_QC result json was written to GCF_000067205.1_ASM6720v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:51,562] [INFO] DFAST_QC completed!
[2024-01-24 13:02:51,562] [INFO] Total running time: 0h1m43s