[2024-01-24 15:10:54,365] [INFO] DFAST_QC pipeline started. [2024-01-24 15:10:54,367] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 15:10:54,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference [2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 15:10:56,634] [INFO] Task started: Prodigal [2024-01-24 15:10:56,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fbfd89c-8a54-44e9-b960-a3b643681ad4/GCF_902833085.1_ASM90283308v1_genomic.fna.gz | prodigal -d GCF_902833085.1_ASM90283308v1_genomic.fna/cds.fna -a GCF_902833085.1_ASM90283308v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 15:11:21,109] [INFO] Task succeeded: Prodigal [2024-01-24 15:11:21,109] [INFO] Task started: HMMsearch [2024-01-24 15:11:21,109] [INFO] Running command: hmmsearch --tblout GCF_902833085.1_ASM90283308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/reference_markers.hmm GCF_902833085.1_ASM90283308v1_genomic.fna/protein.faa > /dev/null [2024-01-24 15:11:21,500] [INFO] Task succeeded: HMMsearch [2024-01-24 15:11:21,502] [INFO] Found 6/6 markers. [2024-01-24 15:11:21,567] [INFO] Query marker FASTA was written to GCF_902833085.1_ASM90283308v1_genomic.fna/markers.fasta [2024-01-24 15:11:21,568] [INFO] Task started: Blastn [2024-01-24 15:11:21,568] [INFO] Running command: blastn -query GCF_902833085.1_ASM90283308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/reference_markers.fasta -out GCF_902833085.1_ASM90283308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:11:22,635] [INFO] Task succeeded: Blastn [2024-01-24 15:11:22,638] [INFO] Selected 9 target genomes. [2024-01-24 15:11:22,639] [INFO] Target genome list was writen to GCF_902833085.1_ASM90283308v1_genomic.fna/target_genomes.txt [2024-01-24 15:11:22,657] [INFO] Task started: fastANI [2024-01-24 15:11:22,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbfd89c-8a54-44e9-b960-a3b643681ad4/GCF_902833085.1_ASM90283308v1_genomic.fna.gz --refList GCF_902833085.1_ASM90283308v1_genomic.fna/target_genomes.txt --output GCF_902833085.1_ASM90283308v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 15:11:43,577] [INFO] Task succeeded: fastANI [2024-01-24 15:11:43,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 15:11:43,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 15:11:43,592] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold) [2024-01-24 15:11:43,592] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 15:11:43,592] [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 Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 100.0 2573 2574 95 conclusive Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 99.9661 2467 2574 95 conclusive Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 94.7482 2051 2574 95 below_threshold Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002097715.1 265293 101571 type True 94.7453 2124 2574 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 91.3024 1955 2574 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 88.9288 1623 2574 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 88.3923 1704 2574 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.6466 1397 2574 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.7949 1180 2574 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 15:11:43,594] [INFO] DFAST Taxonomy check result was written to GCF_902833085.1_ASM90283308v1_genomic.fna/tc_result.tsv [2024-01-24 15:11:43,595] [INFO] ===== Taxonomy check completed ===== [2024-01-24 15:11:43,595] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 15:11:43,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/checkm_data [2024-01-24 15:11:43,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 15:11:43,667] [INFO] Task started: CheckM [2024-01-24 15:11:43,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833085.1_ASM90283308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833085.1_ASM90283308v1_genomic.fna/checkm_input GCF_902833085.1_ASM90283308v1_genomic.fna/checkm_result [2024-01-24 15:12:56,662] [INFO] Task succeeded: CheckM [2024-01-24 15:12:56,664] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 15:12:56,687] [INFO] ===== Completeness check finished ===== [2024-01-24 15:12:56,687] [INFO] ===== Start GTDB Search ===== [2024-01-24 15:12:56,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833085.1_ASM90283308v1_genomic.fna/markers.fasta) [2024-01-24 15:12:56,688] [INFO] Task started: Blastn [2024-01-24 15:12:56,688] [INFO] Running command: blastn -query GCF_902833085.1_ASM90283308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9ef1a9-8cd5-4597-826a-e74f035fd24c/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833085.1_ASM90283308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:12:58,805] [INFO] Task succeeded: Blastn [2024-01-24 15:12:58,809] [INFO] Selected 9 target genomes. [2024-01-24 15:12:58,809] [INFO] Target genome list was writen to GCF_902833085.1_ASM90283308v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 15:12:58,835] [INFO] Task started: fastANI [2024-01-24 15:12:58,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbfd89c-8a54-44e9-b960-a3b643681ad4/GCF_902833085.1_ASM90283308v1_genomic.fna.gz --refList GCF_902833085.1_ASM90283308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833085.1_ASM90283308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 15:13:20,447] [INFO] Task succeeded: fastANI [2024-01-24 15:13:20,461] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 15:13:20,461] [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_000959245.1 s__Burkholderia ubonensis 96.6206 2106 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 conclusive GCF_002097715.1 s__Burkholderia acidophila 94.7217 2127 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_902830275.1 s__Burkholderia stagnalis 91.2684 1959 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 - GCF_004343775.1 s__Burkholderia sp004343775 91.1056 1962 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003854275.1 s__Burkholderia sp003854275 90.3523 1744 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_902499075.1 s__Burkholderia pseudomultivorans 88.9165 1625 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_003853645.1 s__Burkholderia sp003853645 88.6493 1722 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCA_001883705.1 s__Burkholderia catarinensis 88.6279 1567 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499115.1 s__Burkholderia diffusa 88.3801 1693 2574 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 - -------------------------------------------------------------------------------- [2024-01-24 15:13:20,466] [INFO] GTDB search result was written to GCF_902833085.1_ASM90283308v1_genomic.fna/result_gtdb.tsv [2024-01-24 15:13:20,466] [INFO] ===== GTDB Search completed ===== [2024-01-24 15:13:20,469] [INFO] DFAST_QC result json was written to GCF_902833085.1_ASM90283308v1_genomic.fna/dqc_result.json [2024-01-24 15:13:20,469] [INFO] DFAST_QC completed! [2024-01-24 15:13:20,469] [INFO] Total running time: 0h2m26s