[2024-01-24 12:47:08,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:08,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:08,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference
[2024-01-24 12:47:10,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:10,099] [INFO] Task started: Prodigal
[2024-01-24 12:47:10,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg20d73aff-f9a6-4bce-8ed6-c12e077d87e6/GCF_007990955.1_ASM799095v1_genomic.fna.gz | prodigal -d GCF_007990955.1_ASM799095v1_genomic.fna/cds.fna -a GCF_007990955.1_ASM799095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:21,207] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:21,208] [INFO] Task started: HMMsearch
[2024-01-24 12:47:21,208] [INFO] Running command: hmmsearch --tblout GCF_007990955.1_ASM799095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/reference_markers.hmm GCF_007990955.1_ASM799095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:21,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:21,559] [INFO] Found 6/6 markers.
[2024-01-24 12:47:21,622] [INFO] Query marker FASTA was written to GCF_007990955.1_ASM799095v1_genomic.fna/markers.fasta
[2024-01-24 12:47:21,623] [INFO] Task started: Blastn
[2024-01-24 12:47:21,623] [INFO] Running command: blastn -query GCF_007990955.1_ASM799095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/reference_markers.fasta -out GCF_007990955.1_ASM799095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:22,477] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:22,480] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:22,481] [INFO] Target genome list was writen to GCF_007990955.1_ASM799095v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:22,486] [INFO] Task started: fastANI
[2024-01-24 12:47:22,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg20d73aff-f9a6-4bce-8ed6-c12e077d87e6/GCF_007990955.1_ASM799095v1_genomic.fna.gz --refList GCF_007990955.1_ASM799095v1_genomic.fna/target_genomes.txt --output GCF_007990955.1_ASM799095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:31,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:31,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:31,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:31,777] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:31,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:31,778] [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 superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	100.0	1533	1534	95	conclusive
Vibrio superstes	strain=G3-29	GCA_003569005.1	198815	198815	type	True	99.9977	1533	1534	95	conclusive
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	87.5059	1072	1534	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	87.453	1067	1534	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	86.46	1053	1534	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	81.357	571	1534	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	81.1398	529	1534	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	80.7975	528	1534	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	79.9115	457	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:31,779] [INFO] DFAST Taxonomy check result was written to GCF_007990955.1_ASM799095v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:31,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:31,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:31,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/checkm_data
[2024-01-24 12:47:31,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:31,825] [INFO] Task started: CheckM
[2024-01-24 12:47:31,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990955.1_ASM799095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990955.1_ASM799095v1_genomic.fna/checkm_input GCF_007990955.1_ASM799095v1_genomic.fna/checkm_result
[2024-01-24 12:48:09,087] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:09,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:09,107] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:09,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:09,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990955.1_ASM799095v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:09,108] [INFO] Task started: Blastn
[2024-01-24 12:48:09,109] [INFO] Running command: blastn -query GCF_007990955.1_ASM799095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae2270e-f18a-4a44-860f-46057fd35ec0/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990955.1_ASM799095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:10,316] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:10,321] [INFO] Selected 6 target genomes.
[2024-01-24 12:48:10,321] [INFO] Target genome list was writen to GCF_007990955.1_ASM799095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:10,324] [INFO] Task started: fastANI
[2024-01-24 12:48:10,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg20d73aff-f9a6-4bce-8ed6-c12e077d87e6/GCF_007990955.1_ASM799095v1_genomic.fna.gz --refList GCF_007990955.1_ASM799095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990955.1_ASM799095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:16,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:16,750] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:16,751] [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_003569005.1	s__Vibrio superstes	99.9977	1533	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001677275.1	s__Vibrio breoganii	92.4139	1127	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	-
GCF_006538565.1	s__Vibrio comitans	87.465	1066	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538525.1	s__Vibrio inusitatus	86.4295	1029	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467185.1	s__Vibrio ezurae	81.2083	520	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001676025.1	s__Vibrio sp001676025	81.1108	539	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:16,752] [INFO] GTDB search result was written to GCF_007990955.1_ASM799095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:16,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:16,756] [INFO] DFAST_QC result json was written to GCF_007990955.1_ASM799095v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:16,757] [INFO] DFAST_QC completed!
[2024-01-24 12:48:16,757] [INFO] Total running time: 0h1m8s