[2024-01-24 14:19:45,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference
[2024-01-24 14:19:47,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,130] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,130] [INFO] Running command: gunzip -c /var/lib/cwl/stgad89a186-dacc-4b6c-b60a-5bdeefbc37fa/GCF_001558495.2_ASM155849v2_genomic.fna.gz | prodigal -d GCF_001558495.2_ASM155849v2_genomic.fna/cds.fna -a GCF_001558495.2_ASM155849v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:00,154] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:00,154] [INFO] Task started: HMMsearch
[2024-01-24 14:20:00,155] [INFO] Running command: hmmsearch --tblout GCF_001558495.2_ASM155849v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/reference_markers.hmm GCF_001558495.2_ASM155849v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:00,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:00,430] [INFO] Found 6/6 markers.
[2024-01-24 14:20:00,482] [INFO] Query marker FASTA was written to GCF_001558495.2_ASM155849v2_genomic.fna/markers.fasta
[2024-01-24 14:20:00,483] [INFO] Task started: Blastn
[2024-01-24 14:20:00,483] [INFO] Running command: blastn -query GCF_001558495.2_ASM155849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/reference_markers.fasta -out GCF_001558495.2_ASM155849v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:01,282] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:01,284] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:01,284] [INFO] Target genome list was writen to GCF_001558495.2_ASM155849v2_genomic.fna/target_genomes.txt
[2024-01-24 14:20:01,291] [INFO] Task started: fastANI
[2024-01-24 14:20:01,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgad89a186-dacc-4b6c-b60a-5bdeefbc37fa/GCF_001558495.2_ASM155849v2_genomic.fna.gz --refList GCF_001558495.2_ASM155849v2_genomic.fna/target_genomes.txt --output GCF_001558495.2_ASM155849v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:14,145] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:14,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:14,161] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:20:14,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:14,161] [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	100.0	1714	1716	95	conclusive
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	99.9996	1707	1716	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001998785.1	670	670	type	True	99.9792	1660	1716	95	conclusive
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	99.9768	1661	1716	95	conclusive
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	99.961	1641	1716	95	conclusive
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	83.6032	948	1716	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.7121	413	1716	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.5269	404	1716	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.4653	506	1716	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.4276	494	1716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,163] [INFO] DFAST Taxonomy check result was written to GCF_001558495.2_ASM155849v2_genomic.fna/tc_result.tsv
[2024-01-24 14:20:14,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:14,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:14,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/checkm_data
[2024-01-24 14:20:14,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:14,231] [INFO] Task started: CheckM
[2024-01-24 14:20:14,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001558495.2_ASM155849v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001558495.2_ASM155849v2_genomic.fna/checkm_input GCF_001558495.2_ASM155849v2_genomic.fna/checkm_result
[2024-01-24 14:20:54,089] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:54,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:54,103] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:54,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:54,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001558495.2_ASM155849v2_genomic.fna/markers.fasta)
[2024-01-24 14:20:54,104] [INFO] Task started: Blastn
[2024-01-24 14:20:54,104] [INFO] Running command: blastn -query GCF_001558495.2_ASM155849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1040ae95-f9e3-42e4-ac72-4b562c910e87/dqc_reference/reference_markers_gtdb.fasta -out GCF_001558495.2_ASM155849v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:55,305] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:55,307] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:55,307] [INFO] Target genome list was writen to GCF_001558495.2_ASM155849v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:55,326] [INFO] Task started: fastANI
[2024-01-24 14:20:55,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgad89a186-dacc-4b6c-b60a-5bdeefbc37fa/GCF_001558495.2_ASM155849v2_genomic.fna.gz --refList GCF_001558495.2_ASM155849v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001558495.2_ASM155849v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:10,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:10,894] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:10,894] [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	99.9996	1707	1716	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	86.8615	1290	1716	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	86.1224	1252	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_002163755.1	s__Vibrio campbellii	83.9683	1040	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000817815.1	s__Vibrio owensii	83.8672	1082	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_002906655.1	s__Vibrio hyugaensis	83.8108	1120	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_001591145.1	s__Vibrio harveyi	83.7553	1048	1716	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	83.5473	1047	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002741985.1	s__Vibrio rotiferianus	83.3745	995	1716	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	83.3367	930	1716	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	83.0553	862	1716	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	83.0247	882	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCA_018222805.1	s__Vibrio sp018222805	82.886	850	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:10,895] [INFO] GTDB search result was written to GCF_001558495.2_ASM155849v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:10,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:10,898] [INFO] DFAST_QC result json was written to GCF_001558495.2_ASM155849v2_genomic.fna/dqc_result.json
[2024-01-24 14:21:10,898] [INFO] DFAST_QC completed!
[2024-01-24 14:21:10,898] [INFO] Total running time: 0h1m26s