[2024-01-25 18:11:35,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference
[2024-01-25 18:11:36,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,854] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg410312d8-d84a-4110-a5d7-6cc6bf978389/GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna.gz | prodigal -d GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/cds.fna -a GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:45,545] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:45,546] [INFO] Task started: HMMsearch
[2024-01-25 18:11:45,546] [INFO] Running command: hmmsearch --tblout GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/reference_markers.hmm GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:45,759] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:45,760] [INFO] Found 6/6 markers.
[2024-01-25 18:11:45,792] [INFO] Query marker FASTA was written to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/markers.fasta
[2024-01-25 18:11:45,792] [INFO] Task started: Blastn
[2024-01-25 18:11:45,792] [INFO] Running command: blastn -query GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/markers.fasta -db /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/reference_markers.fasta -out GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:46,534] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:46,537] [INFO] Selected 19 target genomes.
[2024-01-25 18:11:46,537] [INFO] Target genome list was writen to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/target_genomes.txt
[2024-01-25 18:11:46,547] [INFO] Task started: fastANI
[2024-01-25 18:11:46,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg410312d8-d84a-4110-a5d7-6cc6bf978389/GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna.gz --refList GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/target_genomes.txt --output GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:06,624] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:06,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:06,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:06,637] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:12:06,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:06,637] [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 aestuarianus subsp. francensis	strain=02/041	GCA_012395215.1	1443279	28171	type	True	100.0	1397	1398	95	conclusive
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	97.5634	1116	1398	95	conclusive
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	97.5195	1114	1398	95	conclusive
Vibrio anguillarum	strain=NCTC12159	GCA_900452855.1	55601	55601	type	True	82.3149	750	1398	95	below_threshold
Vibrio anguillarum	strain=DSM 21597	GCA_001989995.2	55601	55601	type	True	81.8613	714	1398	95	below_threshold
Vibrio qinghaiensis	strain=Q67	GCA_002257545.1	2025808	2025808	type	True	81.8085	702	1398	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.0789	340	1398	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	79.7487	411	1398	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.7405	326	1398	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.6764	395	1398	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	79.6529	323	1398	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	79.5882	400	1398	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.5456	324	1398	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	79.5328	306	1398	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.4183	307	1398	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	79.2878	370	1398	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	79.2831	360	1398	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.2696	366	1398	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	79.252	351	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:06,639] [INFO] DFAST Taxonomy check result was written to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/tc_result.tsv
[2024-01-25 18:12:06,639] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:06,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:06,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/checkm_data
[2024-01-25 18:12:06,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:06,682] [INFO] Task started: CheckM
[2024-01-25 18:12:06,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/checkm_input GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/checkm_result
[2024-01-25 18:12:36,380] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:36,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:36,407] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:36,407] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:36,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/markers.fasta)
[2024-01-25 18:12:36,408] [INFO] Task started: Blastn
[2024-01-25 18:12:36,408] [INFO] Running command: blastn -query GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/markers.fasta -db /var/lib/cwl/stg38963084-4da9-4280-89e1-1057cb7aac67/dqc_reference/reference_markers_gtdb.fasta -out GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:37,534] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:37,536] [INFO] Selected 24 target genomes.
[2024-01-25 18:12:37,536] [INFO] Target genome list was writen to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:37,561] [INFO] Task started: fastANI
[2024-01-25 18:12:37,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg410312d8-d84a-4110-a5d7-6cc6bf978389/GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna.gz --refList GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/target_genomes_gtdb.txt --output GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:57,735] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:57,749] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:57,749] [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_012395185.1	s__Vibrio aestuarianus	97.5207	1114	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.70	96.75	0.86	0.80	14	conclusive
GCF_001989995.2	s__Vibrio anguillarum	81.841	716	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.39	98.01	0.89	0.80	121	-
GCA_000257205.1	s__Vibrio ordalii	81.6582	632	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.3484	98.90	98.90	0.96	0.96	2	-
GCF_009938225.1	s__Vibrio ponticus	79.8257	345	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_002224265.1	s__Vibrio vulnificus	79.8095	413	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_009938205.1	s__Vibrio panuliri	79.74	326	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_014050145.1	s__Vibrio marinisediminis	79.6529	323	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	79.6309	380	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_011064285.1	s__Vibrio ziniensis	79.6195	392	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	79.5957	399	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_000817815.1	s__Vibrio owensii	79.5815	382	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_013041605.1	s__Vibrio plantisponsor	79.4956	397	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
GCF_011806575.1	s__Vibrio hepatarius_A	79.4944	362	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_009938165.1	s__Vibrio taketomensis	79.4887	372	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_014596725.1	s__Vibrio sp014596725	79.463	395	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_000967545.1	s__Vibrio galatheae	79.4303	355	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	79.3878	344	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_013369385.1	s__Vibrio sp013369385	79.383	354	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	79.3153	367	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_001591105.1	s__Vibrio nereis	79.2957	366	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000827885.1	s__Vibrio renipiscarius	79.2633	352	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003970385.1	s__Vibrio aquaticus	79.2345	378	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272145.2	s__Vibrio sp000272145	79.108	366	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	-
GCF_900167345.1	s__Vibrio cincinnatiensis	78.6991	352	1398	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:57,751] [INFO] GTDB search result was written to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:57,751] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:57,754] [INFO] DFAST_QC result json was written to GCF_944737995.1_Vibrio_aestuarianus_02_041_genomic.fna/dqc_result.json
[2024-01-25 18:12:57,754] [INFO] DFAST_QC completed!
[2024-01-25 18:12:57,755] [INFO] Total running time: 0h1m22s