[2024-01-25 18:07:50,371] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,372] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference
[2024-01-25 18:07:51,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,465] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg49ad1ebe-4004-4f2c-b626-6d162de0f7b2/GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna.gz | prodigal -d GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/cds.fna -a GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:03,543] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:03,543] [INFO] Task started: HMMsearch
[2024-01-25 18:08:03,544] [INFO] Running command: hmmsearch --tblout GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/reference_markers.hmm GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:03,822] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:03,823] [INFO] Found 6/6 markers.
[2024-01-25 18:08:03,863] [INFO] Query marker FASTA was written to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/markers.fasta
[2024-01-25 18:08:03,863] [INFO] Task started: Blastn
[2024-01-25 18:08:03,863] [INFO] Running command: blastn -query GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/reference_markers.fasta -out GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:04,630] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:04,634] [INFO] Selected 29 target genomes.
[2024-01-25 18:08:04,634] [INFO] Target genome list was writen to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/target_genomes.txt
[2024-01-25 18:08:04,663] [INFO] Task started: fastANI
[2024-01-25 18:08:04,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ad1ebe-4004-4f2c-b626-6d162de0f7b2/GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna.gz --refList GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/target_genomes.txt --output GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:28,971] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:28,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:28,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:28,985] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:28,986] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:28,986] [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 hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	100.0	1527	1528	95	conclusive
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.2222	270	1528	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.1348	286	1528	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	80.1022	345	1528	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	80.0534	291	1528	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	80.0324	295	1528	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.0119	246	1528	95	below_threshold
Vibrio mediterranei		GCA_900088415.1	689	689	type	True	80.0071	378	1528	95	below_threshold
Vibrio harveyi	strain=FDAARGOS_109	GCA_001471575.2	669	669	type	True	79.9988	288	1528	95	below_threshold
Vibrio barjaei	strain=3062	GCA_001639065.2	1676683	1676683	type	True	79.9579	384	1528	95	below_threshold
Vibrio hangzhouensis	strain=CGMCC 1.7062	GCA_900107935.1	462991	462991	type	True	79.9126	365	1528	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.9081	225	1528	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.8797	265	1528	95	below_threshold
Vibrio mediterranei	strain=NBRC 15635	GCA_001591125.1	689	689	type	True	79.8766	373	1528	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.8467	302	1528	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	79.843	271	1528	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.6641	249	1528	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	79.6531	225	1528	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.5959	248	1528	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.5209	251	1528	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.4141	263	1528	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	79.4114	257	1528	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	79.4079	283	1528	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	79.2502	270	1528	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	79.2296	270	1528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:28,988] [INFO] DFAST Taxonomy check result was written to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/tc_result.tsv
[2024-01-25 18:08:28,988] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:28,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:28,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/checkm_data
[2024-01-25 18:08:28,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:29,034] [INFO] Task started: CheckM
[2024-01-25 18:08:29,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/checkm_input GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/checkm_result
[2024-01-25 18:09:08,322] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:08,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:08,340] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:08,340] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:08,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/markers.fasta)
[2024-01-25 18:09:08,341] [INFO] Task started: Blastn
[2024-01-25 18:09:08,341] [INFO] Running command: blastn -query GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c14265a-71e3-4111-9fa7-3909eb606b97/dqc_reference/reference_markers_gtdb.fasta -out GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:09,296] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:09,299] [INFO] Selected 33 target genomes.
[2024-01-25 18:09:09,299] [INFO] Target genome list was writen to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:09,333] [INFO] Task started: fastANI
[2024-01-25 18:09:09,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ad1ebe-4004-4f2c-b626-6d162de0f7b2/GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna.gz --refList GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/target_genomes_gtdb.txt --output GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:37,959] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:37,979] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:09:37,979] [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_905175385.1	s__Vibrio sp903986855	80.5808	238	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCF_013369335.1	s__Vibrio sp013369335	80.3028	242	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	80.1993	269	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCA_003263785.1	s__Vibrio variabilis	80.1975	369	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906655.1	s__Vibrio hyugaensis	80.1896	297	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_900089835.1	s__Vibrio thalassae	80.0788	348	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCA_003263775.1	s__Vibrio maritimus	80.0396	379	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088415.1	s__Vibrio mediterranei	80.0005	378	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	98.19	97.23	0.91	0.86	13	-
GCF_001639065.2	s__Vibrio barjaei	79.9939	381	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.1582	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	79.9282	364	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	79.9193	244	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_002224265.1	s__Vibrio vulnificus	79.9181	273	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_002215585.1	s__Shewanella marisflavi	79.8996	51	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_009938165.1	s__Vibrio taketomensis	79.8853	252	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_002741985.1	s__Vibrio rotiferianus	79.85	261	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_011064285.1	s__Vibrio ziniensis	79.8499	225	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001695575.1	s__Vibrio europaeus	79.7943	264	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_004551525.1	s__Vibrio ouci	79.4734	257	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	79.4727	236	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_003415655.1	s__Vibrio maerlii	79.4309	257	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	79.4217	263	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775715.1	s__Vibrio tubiashii_A	79.4161	248	1528	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	79.3411	258	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000189275.1	s__Vibrio sinaloensis_B	79.3232	253	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817815.1	s__Vibrio owensii	79.3103	280	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_001591145.1	s__Vibrio harveyi	79.2453	269	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_013369385.1	s__Vibrio sp013369385	79.2137	248	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635455.1	s__Vibrio sp001635455	79.1983	271	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114545.1	s__Vibrio sp013114545	79.144	256	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169995.1	s__Vibrio sp000169995	78.6862	244	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:37,980] [INFO] GTDB search result was written to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:37,981] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:37,985] [INFO] DFAST_QC result json was written to GCF_921292975.1_V_hippocampi_CECT8226_genomic.fna/dqc_result.json
[2024-01-25 18:09:37,985] [INFO] DFAST_QC completed!
[2024-01-25 18:09:37,985] [INFO] Total running time: 0h1m48s