[2024-01-24 12:40:20,807] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference
[2024-01-24 12:40:22,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,030] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,030] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2421821-f7fa-4209-85f4-6418ac884f01/GCF_000621165.1_ASM62116v1_genomic.fna.gz | prodigal -d GCF_000621165.1_ASM62116v1_genomic.fna/cds.fna -a GCF_000621165.1_ASM62116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:37,425] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:37,425] [INFO] Task started: HMMsearch
[2024-01-24 12:40:37,426] [INFO] Running command: hmmsearch --tblout GCF_000621165.1_ASM62116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/reference_markers.hmm GCF_000621165.1_ASM62116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:37,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:37,723] [INFO] Found 6/6 markers.
[2024-01-24 12:40:37,770] [INFO] Query marker FASTA was written to GCF_000621165.1_ASM62116v1_genomic.fna/markers.fasta
[2024-01-24 12:40:37,771] [INFO] Task started: Blastn
[2024-01-24 12:40:37,771] [INFO] Running command: blastn -query GCF_000621165.1_ASM62116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/reference_markers.fasta -out GCF_000621165.1_ASM62116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:38,589] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:38,593] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:38,593] [INFO] Target genome list was writen to GCF_000621165.1_ASM62116v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:38,615] [INFO] Task started: fastANI
[2024-01-24 12:40:38,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2421821-f7fa-4209-85f4-6418ac884f01/GCF_000621165.1_ASM62116v1_genomic.fna.gz --refList GCF_000621165.1_ASM62116v1_genomic.fna/target_genomes.txt --output GCF_000621165.1_ASM62116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:54,271] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:54,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:54,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:54,288] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:54,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:54,289] [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
Enterovibrio calviensis	strain=DSM 14347	GCA_000621165.1	91359	91359	type	True	100.0	1815	1818	95	conclusive
Enterovibrio norvegicus	strain=DSM 15893	GCA_900115495.1	188144	188144	type	True	82.4719	817	1818	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_014863865.1	2491023	2491023	type	True	82.412	854	1818	95	below_threshold
Enterovibrio baiacu	strain=A649	GCA_004120195.1	2491023	2491023	type	True	82.3892	857	1818	95	below_threshold
Enterovibrio nigricans	strain=DSM 22720	GCA_900167155.1	504469	504469	type	True	80.2307	581	1818	95	below_threshold
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	80.0156	686	1818	95	below_threshold
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	80.014	675	1818	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	79.9823	611	1818	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	79.9446	675	1818	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	78.3945	213	1818	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.3208	214	1818	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	78.2821	143	1818	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.0076	159	1818	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.0035	161	1818	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	77.9592	145	1818	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	77.7769	164	1818	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.3357	191	1818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,290] [INFO] DFAST Taxonomy check result was written to GCF_000621165.1_ASM62116v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:54,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:54,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:54,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/checkm_data
[2024-01-24 12:40:54,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:54,347] [INFO] Task started: CheckM
[2024-01-24 12:40:54,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621165.1_ASM62116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621165.1_ASM62116v1_genomic.fna/checkm_input GCF_000621165.1_ASM62116v1_genomic.fna/checkm_result
[2024-01-24 12:41:43,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:43,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:43,452] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:43,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:43,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621165.1_ASM62116v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:43,453] [INFO] Task started: Blastn
[2024-01-24 12:41:43,453] [INFO] Running command: blastn -query GCF_000621165.1_ASM62116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg197eede7-b5da-4eab-8383-d48c5ae16561/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621165.1_ASM62116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:44,694] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:44,698] [INFO] Selected 12 target genomes.
[2024-01-24 12:41:44,699] [INFO] Target genome list was writen to GCF_000621165.1_ASM62116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:44,724] [INFO] Task started: fastANI
[2024-01-24 12:41:44,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2421821-f7fa-4209-85f4-6418ac884f01/GCF_000621165.1_ASM62116v1_genomic.fna.gz --refList GCF_000621165.1_ASM62116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621165.1_ASM62116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:57,624] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:57,636] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:57,636] [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_000621165.1	s__Enterovibrio calviensis	100.0	1815	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115495.1	s__Enterovibrio norvegicus	82.4701	817	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	97.84	95.33	0.92	0.87	14	-
GCF_004120195.1	s__Enterovibrio baiacu	82.4029	855	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000286835.2	s__Enterovibrio norvegicus_A	82.1588	1043	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.02	98.98	0.97	0.97	3	-
GCF_900167155.1	s__Enterovibrio nigricans	80.2406	580	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.93	99.93	1.00	1.00	2	-
GCF_000333895.2	s__Enterovibrio indicus	80.0158	686	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_001559595.1	s__Enterovibrio coralii	80.003	654	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900060185.1	s__Enterovibrio marinus	79.9774	611	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900055185.1	s__Enterovibrio celer	79.9289	677	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001310415.1	s__Enterovibrio sp001310415	79.7236	590	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
GCA_000755385.1	s__Vibrio maritimus_B	77.6757	175	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.88	95.88	0.85	0.85	2	-
GCA_000755425.1	s__Vibrio maritimus_A	77.6363	195	1818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:57,638] [INFO] GTDB search result was written to GCF_000621165.1_ASM62116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:57,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:57,642] [INFO] DFAST_QC result json was written to GCF_000621165.1_ASM62116v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:57,642] [INFO] DFAST_QC completed!
[2024-01-24 12:41:57,642] [INFO] Total running time: 0h1m37s