[2024-01-24 12:44:18,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:18,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:18,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference
[2024-01-24 12:44:20,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:20,026] [INFO] Task started: Prodigal
[2024-01-24 12:44:20,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg09d378b1-8e3f-48f3-b0ef-b8550bc59e82/GCF_000657795.2_gbh03v02_genomic.fna.gz | prodigal -d GCF_000657795.2_gbh03v02_genomic.fna/cds.fna -a GCF_000657795.2_gbh03v02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:34,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:34,312] [INFO] Task started: HMMsearch
[2024-01-24 12:44:34,312] [INFO] Running command: hmmsearch --tblout GCF_000657795.2_gbh03v02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/reference_markers.hmm GCF_000657795.2_gbh03v02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:34,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:34,600] [INFO] Found 6/6 markers.
[2024-01-24 12:44:34,648] [INFO] Query marker FASTA was written to GCF_000657795.2_gbh03v02_genomic.fna/markers.fasta
[2024-01-24 12:44:34,648] [INFO] Task started: Blastn
[2024-01-24 12:44:34,648] [INFO] Running command: blastn -query GCF_000657795.2_gbh03v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/reference_markers.fasta -out GCF_000657795.2_gbh03v02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:35,781] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:35,785] [INFO] Selected 16 target genomes.
[2024-01-24 12:44:35,786] [INFO] Target genome list was writen to GCF_000657795.2_gbh03v02_genomic.fna/target_genomes.txt
[2024-01-24 12:44:35,837] [INFO] Task started: fastANI
[2024-01-24 12:44:35,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d378b1-8e3f-48f3-b0ef-b8550bc59e82/GCF_000657795.2_gbh03v02_genomic.fna.gz --refList GCF_000657795.2_gbh03v02_genomic.fna/target_genomes.txt --output GCF_000657795.2_gbh03v02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:52,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:52,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:52,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:52,581] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:52,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:52,581] [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
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	100.0	1487	1489	95	conclusive
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	93.2508	1248	1489	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	93.197	1214	1489	95	below_threshold
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	83.5426	893	1489	95	below_threshold
Bordetella holmesii	strain=FDAARGOS_1539	GCA_020735985.1	35814	35814	type	True	83.484	898	1489	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	82.974	827	1489	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900078335.1	123899	123899	type	True	82.9097	818	1489	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	82.8248	791	1489	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.8128	803	1489	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	82.7982	779	1489	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	82.6498	914	1489	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	82.4527	936	1489	95	below_threshold
Bordetella avium	strain=HAMBI_2160	GCA_003350095.1	521	521	type	True	82.4481	772	1489	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	81.3708	866	1489	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.1853	285	1489	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.1098	370	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:52,583] [INFO] DFAST Taxonomy check result was written to GCF_000657795.2_gbh03v02_genomic.fna/tc_result.tsv
[2024-01-24 12:44:52,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:52,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:52,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/checkm_data
[2024-01-24 12:44:52,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:52,626] [INFO] Task started: CheckM
[2024-01-24 12:44:52,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000657795.2_gbh03v02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000657795.2_gbh03v02_genomic.fna/checkm_input GCF_000657795.2_gbh03v02_genomic.fna/checkm_result
[2024-01-24 12:45:36,534] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:36,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,557] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:36,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:36,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000657795.2_gbh03v02_genomic.fna/markers.fasta)
[2024-01-24 12:45:36,559] [INFO] Task started: Blastn
[2024-01-24 12:45:36,559] [INFO] Running command: blastn -query GCF_000657795.2_gbh03v02_genomic.fna/markers.fasta -db /var/lib/cwl/stg5300c620-55b0-4f71-b946-fdd780c4027f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000657795.2_gbh03v02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:38,755] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:38,759] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:38,759] [INFO] Target genome list was writen to GCF_000657795.2_gbh03v02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:38,818] [INFO] Task started: fastANI
[2024-01-24 12:45:38,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d378b1-8e3f-48f3-b0ef-b8550bc59e82/GCF_000657795.2_gbh03v02_genomic.fna.gz --refList GCF_000657795.2_gbh03v02_genomic.fna/target_genomes_gtdb.txt --output GCF_000657795.2_gbh03v02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:52,574] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:52,589] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:52,589] [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_000657795.2	s__Bordetella pseudohinzii	100.0	1487	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	conclusive
GCF_001548475.1	s__Bordetella hinzii	93.1972	1214	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_002261355.1	s__Bordetella sp002261355	85.7154	1008	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000612485.1	s__Bordetella holmesii	83.4589	905	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.96	99.94	1.00	0.99	92	-
GCF_002261335.1	s__Bordetella sp002261335	83.0052	948	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_900078335.1	s__Bordetella trematum	82.9096	818	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	-
GCF_000306945.1	s__Bordetella pertussis	82.7902	779	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002885955.2	s__Achromobacter pulmonis_A	82.7677	931	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_002902905.1	s__Achromobacter sp002902905	82.6794	928	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCF_016127315.1	s__Achromobacter insuavis_A	82.5404	964	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_900445835.1	s__Bordetella avium	82.4435	771	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	-
GCF_002261475.1	s__Bordetella sp002261475	82.1797	868	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:52,591] [INFO] GTDB search result was written to GCF_000657795.2_gbh03v02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:52,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:52,595] [INFO] DFAST_QC result json was written to GCF_000657795.2_gbh03v02_genomic.fna/dqc_result.json
[2024-01-24 12:45:52,595] [INFO] DFAST_QC completed!
[2024-01-24 12:45:52,596] [INFO] Total running time: 0h1m34s