[2024-01-24 13:17:13,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference
[2024-01-24 13:17:15,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,223] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg47bffaee-e34f-4f6a-bfb8-68717000d322/GCF_003076355.1_ASM307635v1_genomic.fna.gz | prodigal -d GCF_003076355.1_ASM307635v1_genomic.fna/cds.fna -a GCF_003076355.1_ASM307635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:24,055] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:24,056] [INFO] Task started: HMMsearch
[2024-01-24 13:17:24,056] [INFO] Running command: hmmsearch --tblout GCF_003076355.1_ASM307635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/reference_markers.hmm GCF_003076355.1_ASM307635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:24,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:24,336] [INFO] Found 6/6 markers.
[2024-01-24 13:17:24,371] [INFO] Query marker FASTA was written to GCF_003076355.1_ASM307635v1_genomic.fna/markers.fasta
[2024-01-24 13:17:24,371] [INFO] Task started: Blastn
[2024-01-24 13:17:24,371] [INFO] Running command: blastn -query GCF_003076355.1_ASM307635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/reference_markers.fasta -out GCF_003076355.1_ASM307635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:25,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:25,656] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:25,657] [INFO] Target genome list was writen to GCF_003076355.1_ASM307635v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:25,663] [INFO] Task started: fastANI
[2024-01-24 13:17:25,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg47bffaee-e34f-4f6a-bfb8-68717000d322/GCF_003076355.1_ASM307635v1_genomic.fna.gz --refList GCF_003076355.1_ASM307635v1_genomic.fna/target_genomes.txt --output GCF_003076355.1_ASM307635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:34,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:34,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:34,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:34,795] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:17:34,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:34,796] [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. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	100.0	1078	1078	95	conclusive
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	99.9904	1076	1078	95	conclusive
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	99.9479	1038	1078	95	conclusive
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	93.5289	914	1078	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	93.3903	955	1078	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	93.3631	958	1078	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	93.0772	930	1078	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	92.9695	629	1078	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	91.1883	954	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:34,797] [INFO] DFAST Taxonomy check result was written to GCF_003076355.1_ASM307635v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:34,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:34,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:34,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/checkm_data
[2024-01-24 13:17:34,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:34,839] [INFO] Task started: CheckM
[2024-01-24 13:17:34,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003076355.1_ASM307635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003076355.1_ASM307635v1_genomic.fna/checkm_input GCF_003076355.1_ASM307635v1_genomic.fna/checkm_result
[2024-01-24 13:18:23,515] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:23,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,537] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:23,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:23,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003076355.1_ASM307635v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:23,538] [INFO] Task started: Blastn
[2024-01-24 13:18:23,538] [INFO] Running command: blastn -query GCF_003076355.1_ASM307635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg722e3e93-dbac-4827-b389-610a93901fd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003076355.1_ASM307635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:25,826] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:25,830] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:25,830] [INFO] Target genome list was writen to GCF_003076355.1_ASM307635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:25,848] [INFO] Task started: fastANI
[2024-01-24 13:18:25,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg47bffaee-e34f-4f6a-bfb8-68717000d322/GCF_003076355.1_ASM307635v1_genomic.fna.gz --refList GCF_003076355.1_ASM307635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003076355.1_ASM307635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:36,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:36,784] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:18:36,785] [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_002240565.1	s__Clavibacter insidiosus	99.9904	1076	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.26	95.88	0.97	0.89	7	inconclusive
GCF_000355695.1	s__Clavibacter nebraskensis	95.1652	954	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.1408	99.97	99.95	1.00	1.00	6	inconclusive
GCF_016907085.1	s__Clavibacter michiganensis_O	94.204	963	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168345.1	s__Clavibacter michiganensis	93.4525	949	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_003576185.1	s__Clavibacter phaseoli	93.2106	583	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_015351105.1	s__Clavibacter sp015351105	93.185	965	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002931175.1	s__Clavibacter californiensis	92.9807	913	1078	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	92.9368	938	1078	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	92.6908	934	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_003576405.1	s__Clavibacter sp003576405	92.3625	691	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_001280205.1	s__Clavibacter capsici	91.6264	929	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.16	95.31	0.96	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:36,789] [INFO] GTDB search result was written to GCF_003076355.1_ASM307635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:36,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:36,794] [INFO] DFAST_QC result json was written to GCF_003076355.1_ASM307635v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:36,794] [INFO] DFAST_QC completed!
[2024-01-24 13:18:36,795] [INFO] Total running time: 0h1m23s