[2024-01-24 12:43:54,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference
[2024-01-24 12:43:59,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,335] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg6362bdfe-11de-4234-bb31-9410f90fbbad/GCF_006539085.1_ASM653908v1_genomic.fna.gz | prodigal -d GCF_006539085.1_ASM653908v1_genomic.fna/cds.fna -a GCF_006539085.1_ASM653908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:11,533] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:11,534] [INFO] Task started: HMMsearch
[2024-01-24 12:44:11,534] [INFO] Running command: hmmsearch --tblout GCF_006539085.1_ASM653908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/reference_markers.hmm GCF_006539085.1_ASM653908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:11,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:11,789] [INFO] Found 6/6 markers.
[2024-01-24 12:44:11,825] [INFO] Query marker FASTA was written to GCF_006539085.1_ASM653908v1_genomic.fna/markers.fasta
[2024-01-24 12:44:11,825] [INFO] Task started: Blastn
[2024-01-24 12:44:11,826] [INFO] Running command: blastn -query GCF_006539085.1_ASM653908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/reference_markers.fasta -out GCF_006539085.1_ASM653908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:12,701] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:12,705] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:12,705] [INFO] Target genome list was writen to GCF_006539085.1_ASM653908v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:12,734] [INFO] Task started: fastANI
[2024-01-24 12:44:12,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg6362bdfe-11de-4234-bb31-9410f90fbbad/GCF_006539085.1_ASM653908v1_genomic.fna.gz --refList GCF_006539085.1_ASM653908v1_genomic.fna/target_genomes.txt --output GCF_006539085.1_ASM653908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:21,797] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:21,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:21,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:21,808] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:44:21,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:21,808] [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
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	100.0	1346	1350	95	conclusive
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	99.9952	1350	1350	95	conclusive
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	99.995	1350	1350	95	conclusive
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	94.9767	1097	1350	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.0179	707	1350	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.0139	708	1350	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	82.9913	730	1350	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.8085	168	1350	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.7712	186	1350	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.4937	191	1350	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.4089	189	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:21,809] [INFO] DFAST Taxonomy check result was written to GCF_006539085.1_ASM653908v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:21,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:21,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:21,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/checkm_data
[2024-01-24 12:44:21,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:21,852] [INFO] Task started: CheckM
[2024-01-24 12:44:21,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539085.1_ASM653908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539085.1_ASM653908v1_genomic.fna/checkm_input GCF_006539085.1_ASM653908v1_genomic.fna/checkm_result
[2024-01-24 12:45:01,224] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:01,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:01,244] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:01,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:01,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539085.1_ASM653908v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:01,245] [INFO] Task started: Blastn
[2024-01-24 12:45:01,245] [INFO] Running command: blastn -query GCF_006539085.1_ASM653908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4968e545-6a11-43e4-912b-99431cc183e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539085.1_ASM653908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:02,807] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:02,810] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:02,810] [INFO] Target genome list was writen to GCF_006539085.1_ASM653908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:02,832] [INFO] Task started: fastANI
[2024-01-24 12:45:02,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg6362bdfe-11de-4234-bb31-9410f90fbbad/GCF_006539085.1_ASM653908v1_genomic.fna.gz --refList GCF_006539085.1_ASM653908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539085.1_ASM653908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:10,053] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:10,066] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:10,066] [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_003350405.1	s__Gluconacetobacter liquefaciens	99.9952	1350	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_014174165.1	s__Gluconacetobacter dulcium	94.9787	1097	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	88.3174	954	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	88.3049	953	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	88.2287	1005	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	88.0385	960	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174255.1	s__Gluconacetobacter sacchari	86.7815	936	1350	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:10,068] [INFO] GTDB search result was written to GCF_006539085.1_ASM653908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:10,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:10,072] [INFO] DFAST_QC result json was written to GCF_006539085.1_ASM653908v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:10,073] [INFO] DFAST_QC completed!
[2024-01-24 12:45:10,073] [INFO] Total running time: 0h1m16s