[2024-01-24 12:22:48,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference
[2024-01-24 12:22:49,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,261] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg9da29437-b1c5-4934-a7ab-a786310090e3/GCF_900460165.1_51765_C01_genomic.fna.gz | prodigal -d GCF_900460165.1_51765_C01_genomic.fna/cds.fna -a GCF_900460165.1_51765_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:02,487] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:02,487] [INFO] Task started: HMMsearch
[2024-01-24 12:23:02,487] [INFO] Running command: hmmsearch --tblout GCF_900460165.1_51765_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/reference_markers.hmm GCF_900460165.1_51765_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:02,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:02,736] [INFO] Found 6/6 markers.
[2024-01-24 12:23:02,777] [INFO] Query marker FASTA was written to GCF_900460165.1_51765_C01_genomic.fna/markers.fasta
[2024-01-24 12:23:02,777] [INFO] Task started: Blastn
[2024-01-24 12:23:02,777] [INFO] Running command: blastn -query GCF_900460165.1_51765_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/reference_markers.fasta -out GCF_900460165.1_51765_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:03,502] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:03,505] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:03,505] [INFO] Target genome list was writen to GCF_900460165.1_51765_C01_genomic.fna/target_genomes.txt
[2024-01-24 12:23:03,516] [INFO] Task started: fastANI
[2024-01-24 12:23:03,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg9da29437-b1c5-4934-a7ab-a786310090e3/GCF_900460165.1_51765_C01_genomic.fna.gz --refList GCF_900460165.1_51765_C01_genomic.fna/target_genomes.txt --output GCF_900460165.1_51765_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:19,270] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:19,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:19,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:19,278] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:23:19,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:19,279] [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 harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	100.0	1871	1874	95	conclusive
Vibrio harveyi	strain=FDAARGOS_109	GCA_001471575.2	669	669	type	True	99.9968	1867	1874	95	conclusive
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	99.9338	1740	1874	95	conclusive
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	99.8861	1711	1874	95	conclusive
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	90.2696	1444	1874	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	89.0034	1273	1874	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	88.5488	1277	1874	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.5559	837	1874	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.8986	520	1874	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.5438	469	1874	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.3299	460	1874	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.8115	569	1874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:19,280] [INFO] DFAST Taxonomy check result was written to GCF_900460165.1_51765_C01_genomic.fna/tc_result.tsv
[2024-01-24 12:23:19,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:19,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:19,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/checkm_data
[2024-01-24 12:23:19,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:19,333] [INFO] Task started: CheckM
[2024-01-24 12:23:19,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460165.1_51765_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460165.1_51765_C01_genomic.fna/checkm_input GCF_900460165.1_51765_C01_genomic.fna/checkm_result
[2024-01-24 12:24:00,838] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:00,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,854] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:00,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:00,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460165.1_51765_C01_genomic.fna/markers.fasta)
[2024-01-24 12:24:00,855] [INFO] Task started: Blastn
[2024-01-24 12:24:00,855] [INFO] Running command: blastn -query GCF_900460165.1_51765_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3ff142-b957-4e17-97db-cc2d55b17540/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460165.1_51765_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:01,879] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:01,882] [INFO] Selected 10 target genomes.
[2024-01-24 12:24:01,882] [INFO] Target genome list was writen to GCF_900460165.1_51765_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:01,887] [INFO] Task started: fastANI
[2024-01-24 12:24:01,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg9da29437-b1c5-4934-a7ab-a786310090e3/GCF_900460165.1_51765_C01_genomic.fna.gz --refList GCF_900460165.1_51765_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460165.1_51765_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:16,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:16,136] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:16,136] [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_001591145.1	s__Vibrio harveyi	99.9338	1740	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	conclusive
GCF_000817815.1	s__Vibrio owensii	90.2545	1446	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002163755.1	s__Vibrio campbellii	89.155	1347	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_002741985.1	s__Vibrio rotiferianus	88.5822	1273	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000400365.1	s__Vibrio jasicida	88.4707	1454	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002906655.1	s__Vibrio hyugaensis	87.8883	1454	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000171815.1	s__Vibrio sp000171815	84.5863	950	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000354175.2	s__Vibrio alginolyticus	84.4709	1072	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_900460535.1	s__Vibrio parahaemolyticus	84.0425	1113	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_001048675.1	s__Vibrio diabolicus	83.8549	1038	1874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:16,137] [INFO] GTDB search result was written to GCF_900460165.1_51765_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:16,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:16,141] [INFO] DFAST_QC result json was written to GCF_900460165.1_51765_C01_genomic.fna/dqc_result.json
[2024-01-24 12:24:16,141] [INFO] DFAST_QC completed!
[2024-01-24 12:24:16,141] [INFO] Total running time: 0h1m28s