[2024-01-24 12:14:33,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference
[2024-01-24 12:14:35,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,207] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg169bb321-8977-485b-853b-4245c66cb5cc/GCF_006716865.1_ASM671686v1_genomic.fna.gz | prodigal -d GCF_006716865.1_ASM671686v1_genomic.fna/cds.fna -a GCF_006716865.1_ASM671686v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:49,269] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:49,270] [INFO] Task started: HMMsearch
[2024-01-24 12:14:49,270] [INFO] Running command: hmmsearch --tblout GCF_006716865.1_ASM671686v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/reference_markers.hmm GCF_006716865.1_ASM671686v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:49,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:49,483] [INFO] Found 6/6 markers.
[2024-01-24 12:14:49,541] [INFO] Query marker FASTA was written to GCF_006716865.1_ASM671686v1_genomic.fna/markers.fasta
[2024-01-24 12:14:49,541] [INFO] Task started: Blastn
[2024-01-24 12:14:49,541] [INFO] Running command: blastn -query GCF_006716865.1_ASM671686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/reference_markers.fasta -out GCF_006716865.1_ASM671686v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:50,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:50,189] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:50,189] [INFO] Target genome list was writen to GCF_006716865.1_ASM671686v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:50,208] [INFO] Task started: fastANI
[2024-01-24 12:14:50,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg169bb321-8977-485b-853b-4245c66cb5cc/GCF_006716865.1_ASM671686v1_genomic.fna.gz --refList GCF_006716865.1_ASM671686v1_genomic.fna/target_genomes.txt --output GCF_006716865.1_ASM671686v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:03,451] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:03,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:03,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:03,461] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:03,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:03,461] [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
Roseinatronobacter monicus	strain=DSM 18423	GCA_006716865.1	393481	393481	type	True	100.0	1567	1572	95	conclusive
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	83.547	801	1572	95	below_threshold
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	83.5103	819	1572	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	81.9208	817	1572	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	81.8486	793	1572	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	77.5017	208	1572	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.1268	206	1572	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.0061	207	1572	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.9556	202	1572	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.8869	167	1572	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.6839	170	1572	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.6345	160	1572	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.4792	169	1572	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.4736	115	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,463] [INFO] DFAST Taxonomy check result was written to GCF_006716865.1_ASM671686v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:03,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:03,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:03,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/checkm_data
[2024-01-24 12:15:03,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:03,510] [INFO] Task started: CheckM
[2024-01-24 12:15:03,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716865.1_ASM671686v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716865.1_ASM671686v1_genomic.fna/checkm_input GCF_006716865.1_ASM671686v1_genomic.fna/checkm_result
[2024-01-24 12:15:48,316] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:48,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:48,332] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:48,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:48,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716865.1_ASM671686v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:48,332] [INFO] Task started: Blastn
[2024-01-24 12:15:48,332] [INFO] Running command: blastn -query GCF_006716865.1_ASM671686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca202308-fbe1-4793-aa32-1886eacc411f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716865.1_ASM671686v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:49,342] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:49,345] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:49,345] [INFO] Target genome list was writen to GCF_006716865.1_ASM671686v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:49,353] [INFO] Task started: fastANI
[2024-01-24 12:15:49,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg169bb321-8977-485b-853b-4245c66cb5cc/GCF_006716865.1_ASM671686v1_genomic.fna.gz --refList GCF_006716865.1_ASM671686v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716865.1_ASM671686v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:00,006] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:00,014] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:00,015] [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_006716865.1	s__Roseinatronobacter monicus	100.0	1566	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	95.80	95.17	0.91	0.77	10	conclusive
GCF_001870675.1	s__Roseinatronobacter thiooxidans	83.547	801	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	97.65	95.32	0.95	0.92	3	-
GCA_007126715.1	s__Roseinatronobacter sp007126715	82.6541	657	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.26	99.26	0.87	0.87	2	-
GCF_004366635.1	s__Roseinatronobacter bogoriensis	81.8486	793	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	99.99	0.99	0.99	4	-
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	79.9125	667	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	79.883	533	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_007118445.1	s__Roseinatronobacter sp007118445	79.4205	468	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.03	98.90	0.77	0.72	3	-
GCA_007692585.1	s__Roseinatronobacter sp007692585	79.3503	500	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517585.1	s__Roseinatronobacter calidilacus	79.3409	485	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007131465.1	s__Roseinatronobacter sp007131465	79.2017	389	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117255.1	s__Roseinatronobacter sp007117255	79.1107	366	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695345.1	s__Roseinatronobacter sp007695345	79.0752	504	1572	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,016] [INFO] GTDB search result was written to GCF_006716865.1_ASM671686v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:00,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:00,019] [INFO] DFAST_QC result json was written to GCF_006716865.1_ASM671686v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:00,020] [INFO] DFAST_QC completed!
[2024-01-24 12:16:00,020] [INFO] Total running time: 0h1m26s