[2024-01-25 17:37:20,480] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:20,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:20,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference
[2024-01-25 17:37:21,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:21,648] [INFO] Task started: Prodigal
[2024-01-25 17:37:21,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg98f205f6-4558-4975-ba21-7d7c51b1909d/GCF_021922925.1_ASM2192292v1_genomic.fna.gz | prodigal -d GCF_021922925.1_ASM2192292v1_genomic.fna/cds.fna -a GCF_021922925.1_ASM2192292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:29,263] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:29,264] [INFO] Task started: HMMsearch
[2024-01-25 17:37:29,264] [INFO] Running command: hmmsearch --tblout GCF_021922925.1_ASM2192292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/reference_markers.hmm GCF_021922925.1_ASM2192292v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:29,488] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:29,489] [INFO] Found 6/6 markers.
[2024-01-25 17:37:29,518] [INFO] Query marker FASTA was written to GCF_021922925.1_ASM2192292v1_genomic.fna/markers.fasta
[2024-01-25 17:37:29,518] [INFO] Task started: Blastn
[2024-01-25 17:37:29,519] [INFO] Running command: blastn -query GCF_021922925.1_ASM2192292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/reference_markers.fasta -out GCF_021922925.1_ASM2192292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:30,761] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:30,766] [INFO] Selected 10 target genomes.
[2024-01-25 17:37:30,766] [INFO] Target genome list was writen to GCF_021922925.1_ASM2192292v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:30,769] [INFO] Task started: fastANI
[2024-01-25 17:37:30,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg98f205f6-4558-4975-ba21-7d7c51b1909d/GCF_021922925.1_ASM2192292v1_genomic.fna.gz --refList GCF_021922925.1_ASM2192292v1_genomic.fna/target_genomes.txt --output GCF_021922925.1_ASM2192292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:40,153] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:40,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:40,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:40,162] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:40,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:40,162] [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
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	100.0	1074	1075	95	conclusive
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	93.551	916	1075	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	93.5243	943	1075	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	93.5215	908	1075	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	93.5211	933	1075	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	93.5193	943	1075	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	93.4749	902	1075	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	93.1982	932	1075	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	93.0262	635	1075	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	91.2884	910	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:40,166] [INFO] DFAST Taxonomy check result was written to GCF_021922925.1_ASM2192292v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:40,167] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:40,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:40,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/checkm_data
[2024-01-25 17:37:40,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:40,208] [INFO] Task started: CheckM
[2024-01-25 17:37:40,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021922925.1_ASM2192292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021922925.1_ASM2192292v1_genomic.fna/checkm_input GCF_021922925.1_ASM2192292v1_genomic.fna/checkm_result
[2024-01-25 17:38:25,488] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:25,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:25,508] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:25,509] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:25,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021922925.1_ASM2192292v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:25,510] [INFO] Task started: Blastn
[2024-01-25 17:38:25,510] [INFO] Running command: blastn -query GCF_021922925.1_ASM2192292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg884bce76-bb53-41d0-815b-c1ac1838644a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021922925.1_ASM2192292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:27,678] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:27,681] [INFO] Selected 12 target genomes.
[2024-01-25 17:38:27,681] [INFO] Target genome list was writen to GCF_021922925.1_ASM2192292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:27,687] [INFO] Task started: fastANI
[2024-01-25 17:38:27,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg98f205f6-4558-4975-ba21-7d7c51b1909d/GCF_021922925.1_ASM2192292v1_genomic.fna.gz --refList GCF_021922925.1_ASM2192292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021922925.1_ASM2192292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:39,071] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:39,080] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:39,080] [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_003576185.1	s__Clavibacter phaseoli	96.847	611	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	conclusive
GCF_016907085.1	s__Clavibacter michiganensis_O	93.9851	945	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355695.1	s__Clavibacter nebraskensis	93.6352	907	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	-
GCF_002240565.1	s__Clavibacter insidiosus	93.5498	914	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_900168345.1	s__Clavibacter michiganensis	93.5211	933	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_002931175.1	s__Clavibacter californiensis	93.0631	927	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.71	98.71	0.95	0.95	2	-
GCF_015351105.1	s__Clavibacter sp015351105	93.0045	918	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351075.1	s__Clavibacter sp015351075	92.8778	932	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002151125.1	s__Clavibacter michiganensis_C	92.7314	906	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069225.1	s__Clavibacter sepedonicus	92.6744	900	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_001280205.1	s__Clavibacter capsici	92.1915	907	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCA_002150995.1	s__Clavibacter michiganensis_K	89.9362	914	1075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.44	98.42	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:39,081] [INFO] GTDB search result was written to GCF_021922925.1_ASM2192292v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:39,082] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:39,086] [INFO] DFAST_QC result json was written to GCF_021922925.1_ASM2192292v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:39,086] [INFO] DFAST_QC completed!
[2024-01-25 17:38:39,086] [INFO] Total running time: 0h1m19s