[2024-01-25 18:55:20,726] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:20,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:20,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference
[2024-01-25 18:55:21,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:21,914] [INFO] Task started: Prodigal
[2024-01-25 18:55:21,914] [INFO] Running command: gunzip -c /var/lib/cwl/stge8a3bc75-2665-4fbb-8b0f-c5dca47b1450/GCF_021272385.1_ASM2127238v1_genomic.fna.gz | prodigal -d GCF_021272385.1_ASM2127238v1_genomic.fna/cds.fna -a GCF_021272385.1_ASM2127238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:30,633] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:30,633] [INFO] Task started: HMMsearch
[2024-01-25 18:55:30,633] [INFO] Running command: hmmsearch --tblout GCF_021272385.1_ASM2127238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/reference_markers.hmm GCF_021272385.1_ASM2127238v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:30,875] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:30,876] [INFO] Found 6/6 markers.
[2024-01-25 18:55:30,917] [INFO] Query marker FASTA was written to GCF_021272385.1_ASM2127238v1_genomic.fna/markers.fasta
[2024-01-25 18:55:30,918] [INFO] Task started: Blastn
[2024-01-25 18:55:30,918] [INFO] Running command: blastn -query GCF_021272385.1_ASM2127238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/reference_markers.fasta -out GCF_021272385.1_ASM2127238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:31,629] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:31,632] [INFO] Selected 25 target genomes.
[2024-01-25 18:55:31,632] [INFO] Target genome list was writen to GCF_021272385.1_ASM2127238v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:31,657] [INFO] Task started: fastANI
[2024-01-25 18:55:31,658] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a3bc75-2665-4fbb-8b0f-c5dca47b1450/GCF_021272385.1_ASM2127238v1_genomic.fna.gz --refList GCF_021272385.1_ASM2127238v1_genomic.fna/target_genomes.txt --output GCF_021272385.1_ASM2127238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:51,282] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:51,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:51,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:51,297] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:51,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:51,298] [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 salinus	strain=DNF-1	GCA_021272385.1	2899784	2899784	type	True	100.0	1480	1484	95	conclusive
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	81.0966	94	1484	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	80.3895	135	1484	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	80.1888	143	1484	95	below_threshold
Vibrio viridaestus	strain=LJC006	GCA_003856525.1	2487322	2487322	type	True	79.8748	416	1484	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	79.7889	143	1484	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	79.7487	185	1484	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	79.6609	131	1484	95	below_threshold
Vibrio metschnikovii	strain=NCTC8443	GCA_900460295.1	28172	28172	type	True	79.6021	164	1484	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	79.5111	212	1484	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.4105	159	1484	95	below_threshold
Vibrio quintilis	strain=CECT 7734	GCA_024529975.1	1117707	1117707	type	True	79.3127	226	1484	95	below_threshold
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	78.8861	154	1484	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	78.797	221	1484	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	78.6848	128	1484	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.5357	166	1484	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.4929	164	1484	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	78.4567	167	1484	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_900162645.1	1918946	1918946	type	True	78.3929	129	1484	95	below_threshold
Vibrio quintilis		GCA_900143745.1	1117707	1117707	type	True	78.3651	210	1484	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.1661	138	1484	95	below_threshold
Vibrio ruber	strain=CECT 7878	GCA_900163965.1	184755	184755	type	True	77.9941	202	1484	95	below_threshold
Vibrio rhizosphaerae	strain=DSM 18581	GCA_000711805.1	398736	398736	type	True	77.9526	212	1484	95	below_threshold
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	77.7094	83	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:51,299] [INFO] DFAST Taxonomy check result was written to GCF_021272385.1_ASM2127238v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:51,300] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:51,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:51,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/checkm_data
[2024-01-25 18:55:51,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:51,348] [INFO] Task started: CheckM
[2024-01-25 18:55:51,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021272385.1_ASM2127238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021272385.1_ASM2127238v1_genomic.fna/checkm_input GCF_021272385.1_ASM2127238v1_genomic.fna/checkm_result
[2024-01-25 18:56:21,800] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:21,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:21,824] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:21,824] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:21,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021272385.1_ASM2127238v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:21,826] [INFO] Task started: Blastn
[2024-01-25 18:56:21,826] [INFO] Running command: blastn -query GCF_021272385.1_ASM2127238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1bacb8-ad63-4899-aa46-f9d6871424eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021272385.1_ASM2127238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:22,938] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:22,941] [INFO] Selected 32 target genomes.
[2024-01-25 18:56:22,942] [INFO] Target genome list was writen to GCF_021272385.1_ASM2127238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:22,988] [INFO] Task started: fastANI
[2024-01-25 18:56:22,988] [INFO] Running command: fastANI --query /var/lib/cwl/stge8a3bc75-2665-4fbb-8b0f-c5dca47b1450/GCF_021272385.1_ASM2127238v1_genomic.fna.gz --refList GCF_021272385.1_ASM2127238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021272385.1_ASM2127238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:49,188] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:49,206] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:56:49,206] [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_002157735.2	s__Vibrio aphrogenes	80.3557	120	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856525.1	s__Vibrio viridaestus	79.8856	413	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849855.1	s__Vibrio azureus	79.7987	145	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015686695.1	s__Vibrio nitrifigilis	79.5799	213	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
GCF_015594925.1	s__Vibrio sp002342735	79.5506	140	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.94	96.94	0.92	0.92	2	-
GCF_000176135.1	s__Vibrio coralliilyticus	79.5399	159	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_002218005.2	s__Vibrio algivorus	79.4745	128	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.65	98.65	0.88	0.88	2	-
GCF_002218045.2	s__Vibrio rumoiensis	79.164	130	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806575.1	s__Vibrio hepatarius_A	79.1204	135	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_002196515.1	s__Vibrio gazogenes_A	79.0673	218	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113835.1	s__Vibrio sp013113835	78.9452	140	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967495.1	s__Vibrio neptunius	78.7836	134	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_001399455.2	s__Vibrio bivalvicida	78.7726	137	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_000176155.1	s__Vibrio metschnikovii	78.7716	154	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.65	97.32	0.91	0.86	50	-
GCF_900089835.1	s__Vibrio thalassae	78.6666	130	1484	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	78.4929	164	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_003144035.1	s__Vibrio sp003144035	78.47	167	1484	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	78.462	126	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	-
GCF_900162645.1	s__Vibrio palustris	78.4381	129	1484	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	78.4299	128	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_001676025.1	s__Vibrio sp001676025	78.3876	104	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900143745.1	s__Vibrio quintilis	78.3516	210	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596725.1	s__Vibrio sp014596725	78.2266	171	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_002812955.1	s__Vibrio sp002812955	78.1591	171	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129185.1	s__Vibrio gazogenes	78.1509	193	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	-
GCF_014050145.1	s__Vibrio marinisediminis	78.1387	139	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163965.1	s__Vibrio ruber	78.0434	204	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711805.1	s__Vibrio rhizosphaerae	77.948	213	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114595.1	s__Vibrio sp013114595	77.9289	133	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286955.2	s__Vibrio rumoiensis_A	77.9088	105	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265265.1	s__Photobacterium sanguinicancri	77.758	81	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:49,208] [INFO] GTDB search result was written to GCF_021272385.1_ASM2127238v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:49,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:49,213] [INFO] DFAST_QC result json was written to GCF_021272385.1_ASM2127238v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:49,213] [INFO] DFAST_QC completed!
[2024-01-25 18:56:49,213] [INFO] Total running time: 0h1m28s