[2024-01-24 13:17:15,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference
[2024-01-24 13:17:16,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,421] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,421] [INFO] Running command: gunzip -c /var/lib/cwl/stgd476024f-11cb-42b1-a772-45add37e4b24/GCF_021216655.1_ASM2121665v1_genomic.fna.gz | prodigal -d GCF_021216655.1_ASM2121665v1_genomic.fna/cds.fna -a GCF_021216655.1_ASM2121665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:26,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:26,098] [INFO] Task started: HMMsearch
[2024-01-24 13:17:26,098] [INFO] Running command: hmmsearch --tblout GCF_021216655.1_ASM2121665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/reference_markers.hmm GCF_021216655.1_ASM2121665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:26,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:26,369] [INFO] Found 6/6 markers.
[2024-01-24 13:17:26,402] [INFO] Query marker FASTA was written to GCF_021216655.1_ASM2121665v1_genomic.fna/markers.fasta
[2024-01-24 13:17:26,402] [INFO] Task started: Blastn
[2024-01-24 13:17:26,403] [INFO] Running command: blastn -query GCF_021216655.1_ASM2121665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/reference_markers.fasta -out GCF_021216655.1_ASM2121665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:27,734] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:27,736] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:27,737] [INFO] Target genome list was writen to GCF_021216655.1_ASM2121665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:27,740] [INFO] Task started: fastANI
[2024-01-24 13:17:27,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgd476024f-11cb-42b1-a772-45add37e4b24/GCF_021216655.1_ASM2121665v1_genomic.fna.gz --refList GCF_021216655.1_ASM2121665v1_genomic.fna/target_genomes.txt --output GCF_021216655.1_ASM2121665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,015] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,023] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:17:35,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:35,024] [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	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	100.0	1124	1124	95	conclusive
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	99.9998	1115	1124	95	conclusive
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	99.9868	1090	1124	95	conclusive
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	94.8272	964	1124	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	94.7346	642	1124	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	93.518	942	1124	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	93.3927	940	1124	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	93.3577	955	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,025] [INFO] DFAST Taxonomy check result was written to GCF_021216655.1_ASM2121665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/checkm_data
[2024-01-24 13:17:35,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,065] [INFO] Task started: CheckM
[2024-01-24 13:17:35,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021216655.1_ASM2121665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021216655.1_ASM2121665v1_genomic.fna/checkm_input GCF_021216655.1_ASM2121665v1_genomic.fna/checkm_result
[2024-01-24 13:18:23,156] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:23,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:23,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:23,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021216655.1_ASM2121665v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:23,181] [INFO] Task started: Blastn
[2024-01-24 13:18:23,181] [INFO] Running command: blastn -query GCF_021216655.1_ASM2121665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29252319-6471-4ba1-9eac-6fbb6f166c05/dqc_reference/reference_markers_gtdb.fasta -out GCF_021216655.1_ASM2121665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:25,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:25,193] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:25,193] [INFO] Target genome list was writen to GCF_021216655.1_ASM2121665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:25,216] [INFO] Task started: fastANI
[2024-01-24 13:18:25,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgd476024f-11cb-42b1-a772-45add37e4b24/GCF_021216655.1_ASM2121665v1_genomic.fna.gz --refList GCF_021216655.1_ASM2121665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021216655.1_ASM2121665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:34,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:34,723] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:34,723] [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_900168345.1	s__Clavibacter michiganensis	99.9868	1090	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	conclusive
GCF_002931175.1	s__Clavibacter californiensis	94.7807	939	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.71	98.71	0.95	0.95	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	93.8638	983	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240565.1	s__Clavibacter insidiosus	93.3175	974	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	-
GCF_000355695.1	s__Clavibacter nebraskensis	93.2328	949	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	-
GCF_003576185.1	s__Clavibacter phaseoli	93.2274	584	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_015351075.1	s__Clavibacter sp015351075	92.8743	958	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576405.1	s__Clavibacter sp003576405	92.3396	698	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_002240635.1	s__Clavibacter tessellarius	91.2237	937	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_014775655.1	s__Clavibacter zhangzhiyongii	91.1529	904	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
GCF_001618005.1	s__Clavibacter tessellarius_A	90.7482	887	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,727] [INFO] GTDB search result was written to GCF_021216655.1_ASM2121665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:34,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:34,731] [INFO] DFAST_QC result json was written to GCF_021216655.1_ASM2121665v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:34,732] [INFO] DFAST_QC completed!
[2024-01-24 13:18:34,732] [INFO] Total running time: 0h1m20s