[2024-01-25 18:54:50,920] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:50,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:50,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference
[2024-01-25 18:54:52,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:52,091] [INFO] Task started: Prodigal
[2024-01-25 18:54:52,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg49b253e3-a127-44f8-ac9d-c47b325d2b67/GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna.gz | prodigal -d GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/cds.fna -a GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:02,455] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:02,456] [INFO] Task started: HMMsearch
[2024-01-25 18:55:02,456] [INFO] Running command: hmmsearch --tblout GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/reference_markers.hmm GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:02,668] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:02,669] [INFO] Found 6/6 markers.
[2024-01-25 18:55:02,697] [INFO] Query marker FASTA was written to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/markers.fasta
[2024-01-25 18:55:02,697] [INFO] Task started: Blastn
[2024-01-25 18:55:02,697] [INFO] Running command: blastn -query GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/reference_markers.fasta -out GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:03,455] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:03,463] [INFO] Selected 26 target genomes.
[2024-01-25 18:55:03,463] [INFO] Target genome list was writen to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/target_genomes.txt
[2024-01-25 18:55:03,488] [INFO] Task started: fastANI
[2024-01-25 18:55:03,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b253e3-a127-44f8-ac9d-c47b325d2b67/GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna.gz --refList GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/target_genomes.txt --output GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:22,994] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:22,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:22,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:23,011] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:23,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:23,011] [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
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	100.0	1161	1163	95	conclusive
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	80.0838	112	1163	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.6195	118	1163	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.4202	135	1163	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	79.3419	120	1163	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.2098	125	1163	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	78.9151	126	1163	95	below_threshold
Grimontia hollisae	strain=NCTC11640	GCA_900450635.1	673	673	type	True	78.8931	135	1163	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	78.8331	124	1163	95	below_threshold
Vibrio furnissii	strain=NCTC13120	GCA_900460225.1	29494	29494	type	True	78.8251	174	1163	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	78.7659	149	1163	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	78.7481	162	1163	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.7358	144	1163	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	78.6338	147	1163	95	below_threshold
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	78.5759	103	1163	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.3656	136	1163	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.2754	108	1163	95	below_threshold
Enterovibrio calviensis	strain=DSM 14347	GCA_000621165.1	91359	91359	type	True	78.266	141	1163	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	78.2375	154	1163	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	78.0949	113	1163	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	78.0761	144	1163	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	78.0197	143	1163	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	78.0069	130	1163	95	below_threshold
Vibrio paracholerae	strain=EDC-792	GCA_017169525.1	650003	650003	type	True	77.8894	147	1163	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	77.6824	136	1163	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	77.589	149	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:23,015] [INFO] DFAST Taxonomy check result was written to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/tc_result.tsv
[2024-01-25 18:55:23,015] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:23,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:23,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/checkm_data
[2024-01-25 18:55:23,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:23,088] [INFO] Task started: CheckM
[2024-01-25 18:55:23,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/checkm_input GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/checkm_result
[2024-01-25 18:55:57,917] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:57,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:57,935] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:57,936] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:57,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/markers.fasta)
[2024-01-25 18:55:57,937] [INFO] Task started: Blastn
[2024-01-25 18:55:57,937] [INFO] Running command: blastn -query GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c760cc4-7451-4da4-887b-90368b967076/dqc_reference/reference_markers_gtdb.fasta -out GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:59,110] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:59,113] [INFO] Selected 28 target genomes.
[2024-01-25 18:55:59,113] [INFO] Target genome list was writen to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:59,135] [INFO] Task started: fastANI
[2024-01-25 18:55:59,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg49b253e3-a127-44f8-ac9d-c47b325d2b67/GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna.gz --refList GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/target_genomes_gtdb.txt --output GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:21,516] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:21,533] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:56:21,533] [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_002224265.1	s__Vibrio vulnificus	79.4329	146	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_000176515.1	s__Enterovibrio hollisae	79.0519	123	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
GCF_900460245.1	s__Vibrio fluvialis	78.9413	147	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_009938205.1	s__Vibrio panuliri	78.8594	142	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000176135.1	s__Vibrio coralliilyticus	78.801	123	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013041605.1	s__Vibrio plantisponsor	78.7129	99	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCA_003263845.1	s__Vibrio aestivus	78.5742	95	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026815.1	s__Photobacterium damselae	78.4551	137	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.68	96.10	0.89	0.75	54	-
GCA_000695745.1	s__Vibrio madracius	78.3419	51	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.3378	106	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_001939735.1	s__Photobacterium proteolyticum	78.3053	115	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000417905.1	s__Vibrio natriegens	78.2881	111	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCF_000176175.1	s__Vibrio furnissii	78.2873	152	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_000621165.1	s__Enterovibrio calviensis	78.2752	140	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157795.1	s__Thaumasiovibrio occultus	78.2483	160	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Thaumasiovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166975.1	s__Photobacterium toruni	78.1513	125	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286835.2	s__Enterovibrio norvegicus_A	78.1107	140	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.02	98.98	0.97	0.97	3	-
GCF_900060185.1	s__Enterovibrio marinus	78.061	128	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614885.1	s__Photobacterium sp003614885	78.0551	100	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	78.0357	138	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_003026105.1	s__Photobacterium sp003026105	77.9748	121	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_013113835.1	s__Vibrio sp013113835	77.9481	117	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045095.1	s__Enterovibrio sedimenti	77.9402	136	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	77.8225	127	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711795.1	s__Vibrio pacinii	77.8018	126	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_014841115.1	s__Photobacterium sp014841115	77.7912	98	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.86	98.86	0.94	0.94	2	-
GCF_000333895.2	s__Enterovibrio indicus	77.6948	143	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_000338875.1	s__Vibrio mimicus	77.6146	146	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:21,534] [INFO] GTDB search result was written to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:21,535] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:21,539] [INFO] DFAST_QC result json was written to GCF_921293875.1_V_stylophorae_CECT7929_genomic.fna/dqc_result.json
[2024-01-25 18:56:21,539] [INFO] DFAST_QC completed!
[2024-01-25 18:56:21,539] [INFO] Total running time: 0h1m31s