[2024-01-25 18:00:35,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference
[2024-01-25 18:00:36,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,896] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgb322f264-f952-4c55-9635-6d07ec0d3882/GCF_003569005.1_Vsuperstes_genomic.fna.gz | prodigal -d GCF_003569005.1_Vsuperstes_genomic.fna/cds.fna -a GCF_003569005.1_Vsuperstes_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:47,937] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:47,938] [INFO] Task started: HMMsearch
[2024-01-25 18:00:47,938] [INFO] Running command: hmmsearch --tblout GCF_003569005.1_Vsuperstes_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/reference_markers.hmm GCF_003569005.1_Vsuperstes_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:48,177] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:48,178] [INFO] Found 6/6 markers.
[2024-01-25 18:00:48,215] [INFO] Query marker FASTA was written to GCF_003569005.1_Vsuperstes_genomic.fna/markers.fasta
[2024-01-25 18:00:48,215] [INFO] Task started: Blastn
[2024-01-25 18:00:48,215] [INFO] Running command: blastn -query GCF_003569005.1_Vsuperstes_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/reference_markers.fasta -out GCF_003569005.1_Vsuperstes_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:49,009] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:49,011] [INFO] Selected 9 target genomes.
[2024-01-25 18:00:49,012] [INFO] Target genome list was writen to GCF_003569005.1_Vsuperstes_genomic.fna/target_genomes.txt
[2024-01-25 18:00:49,022] [INFO] Task started: fastANI
[2024-01-25 18:00:49,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgb322f264-f952-4c55-9635-6d07ec0d3882/GCF_003569005.1_Vsuperstes_genomic.fna.gz --refList GCF_003569005.1_Vsuperstes_genomic.fna/target_genomes.txt --output GCF_003569005.1_Vsuperstes_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:58,416] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:58,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:58,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:58,423] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:00:58,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:58,423] [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=G3-29	GCA_003569005.1	198815	198815	type	True	99.9986	1567	1570	95	conclusive
Vibrio superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	99.9772	1535	1570	95	conclusive
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	87.4538	1086	1570	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	87.3395	1069	1570	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	86.3628	1076	1570	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	81.4213	589	1570	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	81.2006	528	1570	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	81.0127	537	1570	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	80.1357	462	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:58,425] [INFO] DFAST Taxonomy check result was written to GCF_003569005.1_Vsuperstes_genomic.fna/tc_result.tsv
[2024-01-25 18:00:58,426] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:58,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:58,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/checkm_data
[2024-01-25 18:00:58,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:58,472] [INFO] Task started: CheckM
[2024-01-25 18:00:58,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003569005.1_Vsuperstes_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003569005.1_Vsuperstes_genomic.fna/checkm_input GCF_003569005.1_Vsuperstes_genomic.fna/checkm_result
[2024-01-25 18:01:34,718] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:34,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:34,735] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:34,735] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:34,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003569005.1_Vsuperstes_genomic.fna/markers.fasta)
[2024-01-25 18:01:34,736] [INFO] Task started: Blastn
[2024-01-25 18:01:34,736] [INFO] Running command: blastn -query GCF_003569005.1_Vsuperstes_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dafa9d3-ec1d-4481-8957-439335ca954b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003569005.1_Vsuperstes_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:35,905] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:35,908] [INFO] Selected 6 target genomes.
[2024-01-25 18:01:35,908] [INFO] Target genome list was writen to GCF_003569005.1_Vsuperstes_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:35,916] [INFO] Task started: fastANI
[2024-01-25 18:01:35,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgb322f264-f952-4c55-9635-6d07ec0d3882/GCF_003569005.1_Vsuperstes_genomic.fna.gz --refList GCF_003569005.1_Vsuperstes_genomic.fna/target_genomes_gtdb.txt --output GCF_003569005.1_Vsuperstes_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:42,502] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:42,507] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:42,508] [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	99.9986	1567	1570	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	92.3881	1145	1570	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	87.3466	1068	1570	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	86.3988	1058	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676025.1	s__Vibrio sp001676025	81.2421	537	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000467185.1	s__Vibrio ezurae	81.2014	518	1570	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:42,511] [INFO] GTDB search result was written to GCF_003569005.1_Vsuperstes_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:42,511] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:42,514] [INFO] DFAST_QC result json was written to GCF_003569005.1_Vsuperstes_genomic.fna/dqc_result.json
[2024-01-25 18:01:42,514] [INFO] DFAST_QC completed!
[2024-01-25 18:01:42,514] [INFO] Total running time: 0h1m7s