[2024-01-24 12:37:37,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference
[2024-01-24 12:37:41,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,019] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,019] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf1399a2-53da-46d2-93be-a5f9cec94605/GCF_900445945.1_52067_A01_genomic.fna.gz | prodigal -d GCF_900445945.1_52067_A01_genomic.fna/cds.fna -a GCF_900445945.1_52067_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:59,856] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:59,857] [INFO] Task started: HMMsearch
[2024-01-24 12:37:59,857] [INFO] Running command: hmmsearch --tblout GCF_900445945.1_52067_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/reference_markers.hmm GCF_900445945.1_52067_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:00,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:00,154] [INFO] Found 6/6 markers.
[2024-01-24 12:38:00,193] [INFO] Query marker FASTA was written to GCF_900445945.1_52067_A01_genomic.fna/markers.fasta
[2024-01-24 12:38:00,194] [INFO] Task started: Blastn
[2024-01-24 12:38:00,194] [INFO] Running command: blastn -query GCF_900445945.1_52067_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/reference_markers.fasta -out GCF_900445945.1_52067_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:01,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:01,252] [INFO] Selected 13 target genomes.
[2024-01-24 12:38:01,253] [INFO] Target genome list was writen to GCF_900445945.1_52067_A01_genomic.fna/target_genomes.txt
[2024-01-24 12:38:01,264] [INFO] Task started: fastANI
[2024-01-24 12:38:01,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1399a2-53da-46d2-93be-a5f9cec94605/GCF_900445945.1_52067_A01_genomic.fna.gz --refList GCF_900445945.1_52067_A01_genomic.fna/target_genomes.txt --output GCF_900445945.1_52067_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:14,826] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:14,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:14,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:14,844] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:14,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:14,845] [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 trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	100.0	1497	1499	95	conclusive
Bordetella trematum	strain=NCTC12995	GCA_900078335.1	123899	123899	type	True	99.9729	1463	1499	95	conclusive
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	82.8087	861	1499	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	82.7566	838	1499	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	82.6763	858	1499	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	81.6814	735	1499	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.591	737	1499	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	81.5284	780	1499	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	81.4247	822	1499	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	81.271	845	1499	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	80.4284	740	1499	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.7453	170	1499	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.4684	319	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:14,848] [INFO] DFAST Taxonomy check result was written to GCF_900445945.1_52067_A01_genomic.fna/tc_result.tsv
[2024-01-24 12:38:14,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:14,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:14,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/checkm_data
[2024-01-24 12:38:14,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:14,895] [INFO] Task started: CheckM
[2024-01-24 12:38:14,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445945.1_52067_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445945.1_52067_A01_genomic.fna/checkm_input GCF_900445945.1_52067_A01_genomic.fna/checkm_result
[2024-01-24 12:39:15,704] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:15,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:15,729] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:15,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:15,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445945.1_52067_A01_genomic.fna/markers.fasta)
[2024-01-24 12:39:15,730] [INFO] Task started: Blastn
[2024-01-24 12:39:15,730] [INFO] Running command: blastn -query GCF_900445945.1_52067_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf435ead-e8cd-4f09-8b58-67008f4ca2dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445945.1_52067_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:17,712] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:17,717] [INFO] Selected 10 target genomes.
[2024-01-24 12:39:17,717] [INFO] Target genome list was writen to GCF_900445945.1_52067_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:17,726] [INFO] Task started: fastANI
[2024-01-24 12:39:17,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1399a2-53da-46d2-93be-a5f9cec94605/GCF_900445945.1_52067_A01_genomic.fna.gz --refList GCF_900445945.1_52067_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445945.1_52067_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:28,613] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:28,626] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:28,626] [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_900078335.1	s__Bordetella trematum	99.9729	1463	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.15	97.27	0.96	0.93	14	conclusive
GCF_000657795.2	s__Bordetella pseudohinzii	82.7219	841	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_001548475.1	s__Bordetella hinzii	82.6619	860	1499	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	81.8627	797	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	81.6688	733	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002261335.1	s__Bordetella sp002261335	81.5584	833	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_902859645.1	s__Achromobacter insuavis	81.4837	813	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_002261475.1	s__Bordetella sp002261475	81.2183	733	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.06	99.06	0.95	0.95	2	-
GCF_017356245.1	s__Bordetella_A petrii_D	81.0803	733	1499	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	80.2553	686	1499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:28,628] [INFO] GTDB search result was written to GCF_900445945.1_52067_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:28,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:28,631] [INFO] DFAST_QC result json was written to GCF_900445945.1_52067_A01_genomic.fna/dqc_result.json
[2024-01-24 12:39:28,631] [INFO] DFAST_QC completed!
[2024-01-24 12:39:28,632] [INFO] Total running time: 0h1m51s