[2024-01-24 13:49:33,573] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference
[2024-01-24 13:49:34,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,968] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dafc73b-2792-4bb1-a29d-d00c458fc6f1/GCF_001591065.1_ASM159106v1_genomic.fna.gz | prodigal -d GCF_001591065.1_ASM159106v1_genomic.fna/cds.fna -a GCF_001591065.1_ASM159106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,363] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,364] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,364] [INFO] Running command: hmmsearch --tblout GCF_001591065.1_ASM159106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/reference_markers.hmm GCF_001591065.1_ASM159106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,696] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,738] [INFO] Query marker FASTA was written to GCF_001591065.1_ASM159106v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,739] [INFO] Task started: Blastn
[2024-01-24 13:49:49,739] [INFO] Running command: blastn -query GCF_001591065.1_ASM159106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/reference_markers.fasta -out GCF_001591065.1_ASM159106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,605] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,610] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:50,611] [INFO] Target genome list was writen to GCF_001591065.1_ASM159106v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,616] [INFO] Task started: fastANI
[2024-01-24 13:49:50,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dafc73b-2792-4bb1-a29d-d00c458fc6f1/GCF_001591065.1_ASM159106v1_genomic.fna.gz --refList GCF_001591065.1_ASM159106v1_genomic.fna/target_genomes.txt --output GCF_001591065.1_ASM159106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:02,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:02,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:02,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:02,810] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:50:02,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:02,811] [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 vulnificus	strain=NBRC 15645	GCA_001591065.1	672	672	type	True	100.0	1559	1563	95	conclusive
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	99.9983	1563	1563	95	conclusive
Vibrio vulnificus	strain=NCTC13647	GCA_900460565.1	672	672	type	True	99.9931	1563	1563	95	conclusive
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	99.9675	1363	1563	95	conclusive
Vibrio cidicii	strain=2756-81	GCA_009763805.1	1763883	1763883	type	True	81.6939	722	1563	95	below_threshold
Vibrio navarrensis	strain=ATCC 51183	GCA_000764325.1	29495	29495	type	True	81.0552	694	1563	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	80.5114	570	1563	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.7852	361	1563	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.7329	351	1563	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.0559	391	1563	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	78.983	445	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:02,813] [INFO] DFAST Taxonomy check result was written to GCF_001591065.1_ASM159106v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:02,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:02,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:02,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/checkm_data
[2024-01-24 13:50:02,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:02,870] [INFO] Task started: CheckM
[2024-01-24 13:50:02,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591065.1_ASM159106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591065.1_ASM159106v1_genomic.fna/checkm_input GCF_001591065.1_ASM159106v1_genomic.fna/checkm_result
[2024-01-24 13:50:48,951] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:48,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:48,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:48,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591065.1_ASM159106v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:48,970] [INFO] Task started: Blastn
[2024-01-24 13:50:48,970] [INFO] Running command: blastn -query GCF_001591065.1_ASM159106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbfed5b8-9722-4f03-83ad-d7de3a291976/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591065.1_ASM159106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:50,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:50,196] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:50,196] [INFO] Target genome list was writen to GCF_001591065.1_ASM159106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:50,205] [INFO] Task started: fastANI
[2024-01-24 13:50:50,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dafc73b-2792-4bb1-a29d-d00c458fc6f1/GCF_001591065.1_ASM159106v1_genomic.fna.gz --refList GCF_001591065.1_ASM159106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591065.1_ASM159106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:00,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:00,739] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:00,739] [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_002224265.1	s__Vibrio vulnificus	99.9983	1563	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	conclusive
GCF_013369385.1	s__Vibrio sp013369385	91.8004	1174	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763805.1	s__Vibrio cidicii	81.699	723	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.20	97.77	0.90	0.87	8	-
GCA_015767675.1	s__Vibrio sp000960595	81.2248	711	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_000764325.1	s__Vibrio navarrensis	81.0509	692	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.3805	98.19	97.06	0.93	0.87	22	-
GCF_001591145.1	s__Vibrio harveyi	80.5304	524	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000817815.1	s__Vibrio owensii	80.4865	574	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_900460535.1	s__Vibrio parahaemolyticus	80.4534	561	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCA_018223135.1	s__Vibrio sp018223135	79.4918	424	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938165.1	s__Vibrio taketomensis	79.4335	375	1563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:00,741] [INFO] GTDB search result was written to GCF_001591065.1_ASM159106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:00,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:00,744] [INFO] DFAST_QC result json was written to GCF_001591065.1_ASM159106v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:00,745] [INFO] DFAST_QC completed!
[2024-01-24 13:51:00,745] [INFO] Total running time: 0h1m27s