[2023-03-18 01:28:57,495] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:28:57,495] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:28:57,496] [INFO] DQC Reference Directory: /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference
[2023-03-18 01:29:02,037] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:29:02,038] [INFO] Task started: Prodigal
[2023-03-18 01:29:02,038] [INFO] Running command: cat /var/lib/cwl/stg2cc0a8ba-640d-4a2a-9331-d44ae803b1bf/OceanDNA-b35316.fa | prodigal -d OceanDNA-b35316/cds.fna -a OceanDNA-b35316/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:29:25,565] [INFO] Task succeeded: Prodigal
[2023-03-18 01:29:25,565] [INFO] Task started: HMMsearch
[2023-03-18 01:29:25,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b35316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/reference_markers.hmm OceanDNA-b35316/protein.faa > /dev/null
[2023-03-18 01:29:25,873] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:29:25,874] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2cc0a8ba-640d-4a2a-9331-d44ae803b1bf/OceanDNA-b35316.fa]
[2023-03-18 01:29:25,900] [INFO] Query marker FASTA was written to OceanDNA-b35316/markers.fasta
[2023-03-18 01:29:25,901] [INFO] Task started: Blastn
[2023-03-18 01:29:25,901] [INFO] Running command: blastn -query OceanDNA-b35316/markers.fasta -db /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/reference_markers.fasta -out OceanDNA-b35316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:29:29,496] [INFO] Task succeeded: Blastn
[2023-03-18 01:29:29,496] [INFO] Selected 10 target genomes.
[2023-03-18 01:29:29,497] [INFO] Target genome list was writen to OceanDNA-b35316/target_genomes.txt
[2023-03-18 01:29:29,520] [INFO] Task started: fastANI
[2023-03-18 01:29:29,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc0a8ba-640d-4a2a-9331-d44ae803b1bf/OceanDNA-b35316.fa --refList OceanDNA-b35316/target_genomes.txt --output OceanDNA-b35316/fastani_result.tsv --threads 1
[2023-03-18 01:29:38,855] [INFO] Task succeeded: fastANI
[2023-03-18 01:29:38,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:29:38,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:29:38,863] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-03-18 01:29:38,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:29:38,863] [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 parahaemolyticus		GCA_001558495.2	670	670	type	True	98.3098	1278	1354	95	conclusive
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	98.3045	1275	1354	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001998785.1	670	670	type	True	98.3036	1269	1354	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	98.2926	1271	1354	95	conclusive
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	98.2758	1268	1354	95	conclusive
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.5162	781	1354	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.0896	302	1354	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.0455	308	1354	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	78.855	370	1354	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	78.6726	385	1354	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:29:38,863] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35316/tc_result.tsv
[2023-03-18 01:29:38,863] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:29:38,863] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:29:38,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/checkm_data
[2023-03-18 01:29:38,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:29:38,870] [INFO] Task started: CheckM
[2023-03-18 01:29:38,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35316/checkm_input OceanDNA-b35316/checkm_result
[2023-03-18 01:30:40,010] [INFO] Task succeeded: CheckM
[2023-03-18 01:30:40,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:30:40,013] [INFO] ===== Completeness check finished =====
[2023-03-18 01:30:40,013] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:30:40,013] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35316/markers.fasta)
[2023-03-18 01:30:40,015] [INFO] Task started: Blastn
[2023-03-18 01:30:40,015] [INFO] Running command: blastn -query OceanDNA-b35316/markers.fasta -db /var/lib/cwl/stga112ffdb-9bbf-4ed6-b569-525df0d0adaf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:30:40,967] [INFO] Task succeeded: Blastn
[2023-03-18 01:30:40,968] [INFO] Selected 13 target genomes.
[2023-03-18 01:30:40,968] [INFO] Target genome list was writen to OceanDNA-b35316/target_genomes_gtdb.txt
[2023-03-18 01:30:40,981] [INFO] Task started: fastANI
[2023-03-18 01:30:40,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc0a8ba-640d-4a2a-9331-d44ae803b1bf/OceanDNA-b35316.fa --refList OceanDNA-b35316/target_genomes_gtdb.txt --output OceanDNA-b35316/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:30:54,066] [INFO] Task succeeded: fastANI
[2023-03-18 01:30:54,074] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:30:54,074] [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_900460535.1	s__Vibrio parahaemolyticus	98.3045	1275	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	conclusive
GCA_001048675.1	s__Vibrio diabolicus	85.5117	1076	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_000354175.2	s__Vibrio alginolyticus	84.7373	995	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_000817815.1	s__Vibrio owensii	83.0214	888	1354	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	82.9769	827	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001591145.1	s__Vibrio harveyi	82.7485	898	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000400365.1	s__Vibrio jasicida	82.7426	863	1354	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	82.6681	879	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_002741985.1	s__Vibrio rotiferianus	82.6118	806	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000417905.1	s__Vibrio natriegens	82.5184	777	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.60	95.57	0.95	0.90	11	-
GCA_018223135.1	s__Vibrio sp018223135	82.3845	728	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222805.1	s__Vibrio sp018222805	82.174	738	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905175385.1	s__Vibrio sp903986855	81.9884	715	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2023-03-18 01:30:54,074] [INFO] GTDB search result was written to OceanDNA-b35316/result_gtdb.tsv
[2023-03-18 01:30:54,075] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:30:54,076] [INFO] DFAST_QC result json was written to OceanDNA-b35316/dqc_result.json
[2023-03-18 01:30:54,076] [INFO] DFAST_QC completed!
[2023-03-18 01:30:54,076] [INFO] Total running time: 0h1m57s