[2024-01-24 11:43:38,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:38,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:38,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference
[2024-01-24 11:43:39,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:39,358] [INFO] Task started: Prodigal
[2024-01-24 11:43:39,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg62c5a518-5f81-4c4f-a895-d5d90c8f0705/GCF_002240635.1_ASM224063v1_genomic.fna.gz | prodigal -d GCF_002240635.1_ASM224063v1_genomic.fna/cds.fna -a GCF_002240635.1_ASM224063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:48,186] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:48,187] [INFO] Task started: HMMsearch
[2024-01-24 11:43:48,187] [INFO] Running command: hmmsearch --tblout GCF_002240635.1_ASM224063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/reference_markers.hmm GCF_002240635.1_ASM224063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:48,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:48,577] [INFO] Found 6/6 markers.
[2024-01-24 11:43:48,605] [INFO] Query marker FASTA was written to GCF_002240635.1_ASM224063v1_genomic.fna/markers.fasta
[2024-01-24 11:43:48,606] [INFO] Task started: Blastn
[2024-01-24 11:43:48,606] [INFO] Running command: blastn -query GCF_002240635.1_ASM224063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/reference_markers.fasta -out GCF_002240635.1_ASM224063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:49,874] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:49,877] [INFO] Selected 10 target genomes.
[2024-01-24 11:43:49,877] [INFO] Target genome list was writen to GCF_002240635.1_ASM224063v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:49,895] [INFO] Task started: fastANI
[2024-01-24 11:43:49,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg62c5a518-5f81-4c4f-a895-d5d90c8f0705/GCF_002240635.1_ASM224063v1_genomic.fna.gz --refList GCF_002240635.1_ASM224063v1_genomic.fna/target_genomes.txt --output GCF_002240635.1_ASM224063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:59,497] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:59,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:59,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:59,507] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:59,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:59,507] [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 michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	100.0	1102	1105	95	conclusive
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	99.9984	1094	1105	95	conclusive
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	91.354	927	1105	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	91.2037	912	1105	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	91.112	953	1105	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	91.1055	948	1105	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	91.1035	624	1105	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	91.0522	965	1105	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	91.0478	939	1105	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	90.8419	929	1105	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:59,509] [INFO] DFAST Taxonomy check result was written to GCF_002240635.1_ASM224063v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:59,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:59,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:59,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/checkm_data
[2024-01-24 11:43:59,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:59,547] [INFO] Task started: CheckM
[2024-01-24 11:43:59,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002240635.1_ASM224063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002240635.1_ASM224063v1_genomic.fna/checkm_input GCF_002240635.1_ASM224063v1_genomic.fna/checkm_result
[2024-01-24 11:44:46,994] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:46,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:47,015] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:47,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:47,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002240635.1_ASM224063v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:47,016] [INFO] Task started: Blastn
[2024-01-24 11:44:47,017] [INFO] Running command: blastn -query GCF_002240635.1_ASM224063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c03cdce-7b13-411a-9b39-b3ac955a45be/dqc_reference/reference_markers_gtdb.fasta -out GCF_002240635.1_ASM224063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:49,189] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:49,192] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:49,192] [INFO] Target genome list was writen to GCF_002240635.1_ASM224063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:49,202] [INFO] Task started: fastANI
[2024-01-24 11:44:49,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg62c5a518-5f81-4c4f-a895-d5d90c8f0705/GCF_002240635.1_ASM224063v1_genomic.fna.gz --refList GCF_002240635.1_ASM224063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002240635.1_ASM224063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:01,434] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:01,448] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:01,448] [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_002240635.1	s__Clavibacter tessellarius	100.0	1103	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	conclusive
GCF_001618005.1	s__Clavibacter tessellarius_A	93.6518	937	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384945.1	s__Clavibacter sp003384945	91.4775	928	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280205.1	s__Clavibacter capsici	91.4724	955	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
GCF_014775655.1	s__Clavibacter zhangzhiyongii	91.3917	926	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	91.3183	966	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576185.1	s__Clavibacter phaseoli	91.2209	583	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_900168345.1	s__Clavibacter michiganensis	91.1353	946	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_002240565.1	s__Clavibacter insidiosus	91.0718	958	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_003576405.1	s__Clavibacter sp003576405	91.0504	697	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_002931175.1	s__Clavibacter californiensis	90.8215	902	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.71	98.71	0.95	0.95	2	-
GCF_015351075.1	s__Clavibacter sp015351075	90.7877	951	1105	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	90.5234	928	1105	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:01,449] [INFO] GTDB search result was written to GCF_002240635.1_ASM224063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:01,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:01,453] [INFO] DFAST_QC result json was written to GCF_002240635.1_ASM224063v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:01,453] [INFO] DFAST_QC completed!
[2024-01-24 11:45:01,453] [INFO] Total running time: 0h1m23s