[2024-01-24 12:13:43,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:43,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:43,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference
[2024-01-24 12:13:45,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:45,104] [INFO] Task started: Prodigal
[2024-01-24 12:13:45,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a03d932-c0af-4276-8a4a-e411a305ccb7/GCF_024347075.1_ASM2434707v1_genomic.fna.gz | prodigal -d GCF_024347075.1_ASM2434707v1_genomic.fna/cds.fna -a GCF_024347075.1_ASM2434707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:56,035] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:56,036] [INFO] Task started: HMMsearch
[2024-01-24 12:13:56,036] [INFO] Running command: hmmsearch --tblout GCF_024347075.1_ASM2434707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/reference_markers.hmm GCF_024347075.1_ASM2434707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:56,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:56,382] [INFO] Found 6/6 markers.
[2024-01-24 12:13:56,439] [INFO] Query marker FASTA was written to GCF_024347075.1_ASM2434707v1_genomic.fna/markers.fasta
[2024-01-24 12:13:56,439] [INFO] Task started: Blastn
[2024-01-24 12:13:56,439] [INFO] Running command: blastn -query GCF_024347075.1_ASM2434707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/reference_markers.fasta -out GCF_024347075.1_ASM2434707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:57,285] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:57,288] [INFO] Selected 12 target genomes.
[2024-01-24 12:13:57,289] [INFO] Target genome list was writen to GCF_024347075.1_ASM2434707v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:57,294] [INFO] Task started: fastANI
[2024-01-24 12:13:57,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a03d932-c0af-4276-8a4a-e411a305ccb7/GCF_024347075.1_ASM2434707v1_genomic.fna.gz --refList GCF_024347075.1_ASM2434707v1_genomic.fna/target_genomes.txt --output GCF_024347075.1_ASM2434707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:07,926] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:07,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:07,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:07,937] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:07,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:07,938] [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 rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	100.0	1289	1290	95	conclusive
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	81.7265	512	1290	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	81.643	531	1290	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	81.417	615	1290	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	81.3018	493	1290	95	below_threshold
Vibrio halioticoli	strain=IAM 14596	GCA_003568965.1	71388	71388	type	True	81.2545	596	1290	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	81.2061	574	1290	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	81.2031	571	1290	95	below_threshold
Vibrio ezurae	strain=NBRC 102218	GCA_000467185.1	252583	252583	type	True	81.1703	553	1290	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	80.9737	516	1290	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	80.4764	201	1290	95	below_threshold
Vibrio gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	80.4593	301	1290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:07,940] [INFO] DFAST Taxonomy check result was written to GCF_024347075.1_ASM2434707v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:07,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:07,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:07,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/checkm_data
[2024-01-24 12:14:07,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:07,988] [INFO] Task started: CheckM
[2024-01-24 12:14:07,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347075.1_ASM2434707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347075.1_ASM2434707v1_genomic.fna/checkm_input GCF_024347075.1_ASM2434707v1_genomic.fna/checkm_result
[2024-01-24 12:14:46,793] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:46,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:46,822] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:46,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:46,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347075.1_ASM2434707v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:46,824] [INFO] Task started: Blastn
[2024-01-24 12:14:46,824] [INFO] Running command: blastn -query GCF_024347075.1_ASM2434707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed6b443-03d3-42f4-9886-b5c12c3a68d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347075.1_ASM2434707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,145] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,150] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:48,150] [INFO] Target genome list was writen to GCF_024347075.1_ASM2434707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:48,165] [INFO] Task started: fastANI
[2024-01-24 12:14:48,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a03d932-c0af-4276-8a4a-e411a305ccb7/GCF_024347075.1_ASM2434707v1_genomic.fna.gz --refList GCF_024347075.1_ASM2434707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347075.1_ASM2434707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:56,328] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:56,343] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:14:56,344] [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_001676025.1	s__Vibrio sp001676025	82.7161	717	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006538525.1	s__Vibrio inusitatus	81.2874	494	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677275.1	s__Vibrio breoganii	81.2659	569	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_000496695.1	s__Vibrio halioticoli	81.1786	574	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.31	0.94	0.87	3	-
GCF_000467185.1	s__Vibrio ezurae	81.1642	553	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003569005.1	s__Vibrio superstes	81.0109	539	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006538565.1	s__Vibrio comitans	80.9737	516	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	79.1057	190	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009727955.1	s__Aliivibrio fischeri_A	78.3923	194	1290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.1568	98.75	97.87	0.96	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,346] [INFO] GTDB search result was written to GCF_024347075.1_ASM2434707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:56,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:56,350] [INFO] DFAST_QC result json was written to GCF_024347075.1_ASM2434707v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:56,350] [INFO] DFAST_QC completed!
[2024-01-24 12:14:56,350] [INFO] Total running time: 0h1m13s