[2024-01-24 13:45:46,755] [INFO] DFAST_QC pipeline started. [2024-01-24 13:45:46,757] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:45:46,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference [2024-01-24 13:45:48,194] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:45:48,195] [INFO] Task started: Prodigal [2024-01-24 13:45:48,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg03bf4613-7ce7-475f-b7e1-1a3d1b3e8848/GCF_000012945.1_ASM1294v1_genomic.fna.gz | prodigal -d GCF_000012945.1_ASM1294v1_genomic.fna/cds.fna -a GCF_000012945.1_ASM1294v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:46:15,188] [INFO] Task succeeded: Prodigal [2024-01-24 13:46:15,189] [INFO] Task started: HMMsearch [2024-01-24 13:46:15,189] [INFO] Running command: hmmsearch --tblout GCF_000012945.1_ASM1294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/reference_markers.hmm GCF_000012945.1_ASM1294v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:46:15,665] [INFO] Task succeeded: HMMsearch [2024-01-24 13:46:15,666] [INFO] Found 6/6 markers. [2024-01-24 13:46:15,735] [INFO] Query marker FASTA was written to GCF_000012945.1_ASM1294v1_genomic.fna/markers.fasta [2024-01-24 13:46:15,736] [INFO] Task started: Blastn [2024-01-24 13:46:15,736] [INFO] Running command: blastn -query GCF_000012945.1_ASM1294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/reference_markers.fasta -out GCF_000012945.1_ASM1294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:46:16,810] [INFO] Task succeeded: Blastn [2024-01-24 13:46:16,814] [INFO] Selected 17 target genomes. [2024-01-24 13:46:16,814] [INFO] Target genome list was writen to GCF_000012945.1_ASM1294v1_genomic.fna/target_genomes.txt [2024-01-24 13:46:16,816] [INFO] Task started: fastANI [2024-01-24 13:46:16,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg03bf4613-7ce7-475f-b7e1-1a3d1b3e8848/GCF_000012945.1_ASM1294v1_genomic.fna.gz --refList GCF_000012945.1_ASM1294v1_genomic.fna/target_genomes.txt --output GCF_000012945.1_ASM1294v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:46:57,296] [INFO] Task succeeded: fastANI [2024-01-24 13:46:57,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:46:57,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:46:57,316] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:46:57,317] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:46:57,317] [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 lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 100.0 2890 2891 95 conclusive Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 94.5037 2235 2891 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 94.501 2229 2891 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 94.2654 2181 2891 95 below_threshold Burkholderia aenigmatica strain=LMG 13014 GCA_902499175.1 2015348 2015348 suspected-type True 94.2437 2221 2891 95 below_threshold Burkholderia puraquae strain=LMG 29660 GCA_902859845.1 1904757 1904757 type True 94.174 2181 2891 95 below_threshold Burkholderia cepacia strain=UCB 717 GCA_001411495.1 292 292 type True 93.6499 2250 2891 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 93.6051 2196 2891 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 93.5791 2259 2891 95 below_threshold Burkholderia metallica strain=LMG 24068 GCA_902832845.1 488729 488729 type True 93.218 2099 2891 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 92.4891 2078 2891 95 below_threshold Burkholderia arboris GCA_902499125.1 488730 488730 type True 92.4231 2236 2891 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.6826 1920 2891 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.327 1805 2891 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.3036 1730 2891 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.1953 1421 2891 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.1985 1313 2891 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:46:57,319] [INFO] DFAST Taxonomy check result was written to GCF_000012945.1_ASM1294v1_genomic.fna/tc_result.tsv [2024-01-24 13:46:57,320] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:46:57,320] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:46:57,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/checkm_data [2024-01-24 13:46:57,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:46:57,400] [INFO] Task started: CheckM [2024-01-24 13:46:57,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012945.1_ASM1294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012945.1_ASM1294v1_genomic.fna/checkm_input GCF_000012945.1_ASM1294v1_genomic.fna/checkm_result [2024-01-24 13:48:36,733] [INFO] Task succeeded: CheckM [2024-01-24 13:48:36,735] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:48:36,762] [INFO] ===== Completeness check finished ===== [2024-01-24 13:48:36,762] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:48:36,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012945.1_ASM1294v1_genomic.fna/markers.fasta) [2024-01-24 13:48:36,763] [INFO] Task started: Blastn [2024-01-24 13:48:36,763] [INFO] Running command: blastn -query GCF_000012945.1_ASM1294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg476cac26-fb24-4060-b9a9-0dc208216761/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012945.1_ASM1294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:48:38,850] [INFO] Task succeeded: Blastn [2024-01-24 13:48:38,854] [INFO] Selected 12 target genomes. [2024-01-24 13:48:38,854] [INFO] Target genome list was writen to GCF_000012945.1_ASM1294v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:48:38,857] [INFO] Task started: fastANI [2024-01-24 13:48:38,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg03bf4613-7ce7-475f-b7e1-1a3d1b3e8848/GCF_000012945.1_ASM1294v1_genomic.fna.gz --refList GCF_000012945.1_ASM1294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000012945.1_ASM1294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:49:06,349] [INFO] Task succeeded: fastANI [2024-01-24 13:49:06,365] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:49:06,366] [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_000012945.1 s__Burkholderia lata 100.0 2890 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.30 0.88 0.82 11 conclusive GCF_902499335.1 s__Burkholderia lata_B 94.8471 2430 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.27 95.15 0.87 0.83 7 - GCF_000987075.1 s__Burkholderia contaminans 94.527 2226 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_902833045.1 s__Burkholderia sp902833045 94.4608 2069 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.81 96.81 0.81 0.81 2 - GCF_002099195.1 s__Burkholderia puraquae 94.2565 2182 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.50 95.00 0.89 0.80 3 - GCF_902499175.1 s__Burkholderia aenigmatica 94.2524 2220 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.89 95.59 0.85 0.80 12 - GCF_011605345.1 s__Burkholderia sp011605345 93.7334 2321 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001411495.1 s__Burkholderia cepacia 93.6527 2250 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.84 96.33 0.89 0.79 182 - GCF_902832845.1 s__Burkholderia metallica 93.2429 2096 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.19 98.00 0.94 0.86 6 - GCF_001718835.1 s__Burkholderia cepacia_F 92.4036 1827 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003853705.1 s__Burkholderia sp003853705 92.1652 2084 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000292915.1 s__Burkholderia cepacia_D 91.1283 1796 2891 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:49:06,367] [INFO] GTDB search result was written to GCF_000012945.1_ASM1294v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:49:06,368] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:49:06,371] [INFO] DFAST_QC result json was written to GCF_000012945.1_ASM1294v1_genomic.fna/dqc_result.json [2024-01-24 13:49:06,371] [INFO] DFAST_QC completed! [2024-01-24 13:49:06,371] [INFO] Total running time: 0h3m20s