[2024-01-24 13:28:10,378] [INFO] DFAST_QC pipeline started. [2024-01-24 13:28:10,379] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:28:10,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference [2024-01-24 13:28:11,642] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:28:11,643] [INFO] Task started: Prodigal [2024-01-24 13:28:11,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b5e4b04-3384-485c-9897-b69f8064be39/GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna.gz | prodigal -d GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/cds.fna -a GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:28:35,707] [INFO] Task succeeded: Prodigal [2024-01-24 13:28:35,708] [INFO] Task started: HMMsearch [2024-01-24 13:28:35,708] [INFO] Running command: hmmsearch --tblout GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/reference_markers.hmm GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/protein.faa > /dev/null [2024-01-24 13:28:36,186] [INFO] Task succeeded: HMMsearch [2024-01-24 13:28:36,188] [INFO] Found 6/6 markers. [2024-01-24 13:28:36,254] [INFO] Query marker FASTA was written to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/markers.fasta [2024-01-24 13:28:36,255] [INFO] Task started: Blastn [2024-01-24 13:28:36,255] [INFO] Running command: blastn -query GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/markers.fasta -db /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/reference_markers.fasta -out GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:28:37,407] [INFO] Task succeeded: Blastn [2024-01-24 13:28:37,410] [INFO] Selected 18 target genomes. [2024-01-24 13:28:37,410] [INFO] Target genome list was writen to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/target_genomes.txt [2024-01-24 13:28:37,417] [INFO] Task started: fastANI [2024-01-24 13:28:37,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5e4b04-3384-485c-9897-b69f8064be39/GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna.gz --refList GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/target_genomes.txt --output GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:29:17,323] [INFO] Task succeeded: fastANI [2024-01-24 13:29:17,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:29:17,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:29:17,342] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:29:17,342] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:29:17,343] [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 seminalis strain=LMG 24067 GCA_902832885.1 488731 488731 type True 100.0 2632 2634 95 conclusive Burkholderia seminalis GCA_902499165.1 488731 488731 type True 99.9534 2530 2634 95 conclusive Burkholderia arboris GCA_902499125.1 488730 488730 type True 93.5119 2028 2634 95 below_threshold Burkholderia pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 92.7598 1991 2634 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 92.7485 2024 2634 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 92.3287 2108 2634 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 92.2742 2149 2634 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 92.2549 2065 2634 95 below_threshold Burkholderia lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 92.0818 2019 2634 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 91.9649 2183 2634 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 91.9281 2188 2634 95 below_threshold Burkholderia anthina strain=LMG 20980 GCA_902830395.1 179879 179879 suspected-type True 90.8542 1863 2634 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.8148 1881 2634 95 below_threshold Burkholderia anthina GCA_902498995.1 179879 179879 suspected-type True 90.7886 1863 2634 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.8498 1706 2634 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.8137 1748 2634 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.5593 1403 2634 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.1133 1248 2634 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:29:17,344] [INFO] DFAST Taxonomy check result was written to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/tc_result.tsv [2024-01-24 13:29:17,345] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:29:17,345] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:29:17,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/checkm_data [2024-01-24 13:29:17,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:29:17,422] [INFO] Task started: CheckM [2024-01-24 13:29:17,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/checkm_input GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/checkm_result [2024-01-24 13:30:35,497] [INFO] Task succeeded: CheckM [2024-01-24 13:30:35,499] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:30:35,521] [INFO] ===== Completeness check finished ===== [2024-01-24 13:30:35,522] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:30:35,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/markers.fasta) [2024-01-24 13:30:35,523] [INFO] Task started: Blastn [2024-01-24 13:30:35,523] [INFO] Running command: blastn -query GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/markers.fasta -db /var/lib/cwl/stg04f42e5e-09a3-4f41-8495-5c97aeb9faeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:30:37,627] [INFO] Task succeeded: Blastn [2024-01-24 13:30:37,630] [INFO] Selected 15 target genomes. [2024-01-24 13:30:37,630] [INFO] Target genome list was writen to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:30:37,642] [INFO] Task started: fastANI [2024-01-24 13:30:37,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b5e4b04-3384-485c-9897-b69f8064be39/GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna.gz --refList GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/target_genomes_gtdb.txt --output GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:31:11,401] [INFO] Task succeeded: fastANI [2024-01-24 13:31:11,417] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:31:11,417] [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_902832885.1 s__Burkholderia seminalis 100.0 2632 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.92 97.02 0.94 0.87 12 conclusive GCF_902833225.1 s__Burkholderia sp902833225 93.9899 2115 2634 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 93.9247 2090 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499125.1 s__Burkholderia arboris 93.521 2027 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_001028665.1 s__Burkholderia pyrrocinia 92.7666 2023 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.68 95.03 0.81 0.77 21 - GCF_900446215.1 s__Burkholderia cenocepacia 92.6288 2065 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - GCF_902833145.1 s__Burkholderia sp902833145 92.5827 1973 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_001547525.1 s__Burkholderia anthina_A 92.5239 1980 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.44 98.20 0.94 0.91 13 - GCF_016899425.1 s__Burkholderia sp002223185 92.4394 2059 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_902499335.1 s__Burkholderia lata_B 92.1943 2068 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.27 95.15 0.87 0.83 7 - GCF_000012945.1 s__Burkholderia lata 92.0695 2021 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.30 0.88 0.82 11 - GCF_000987075.1 s__Burkholderia contaminans 91.9774 2182 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_001718835.1 s__Burkholderia cepacia_F 91.5671 1766 2634 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 91.2962 1690 2634 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003635165.1 s__Burkholderia sp003635165 90.5398 1880 2634 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 13:31:11,419] [INFO] GTDB search result was written to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/result_gtdb.tsv [2024-01-24 13:31:11,419] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:31:11,423] [INFO] DFAST_QC result json was written to GCF_902832885.1_Burkholderia_seminalis_LMG_24067_genomic.fna/dqc_result.json [2024-01-24 13:31:11,424] [INFO] DFAST_QC completed! [2024-01-24 13:31:11,424] [INFO] Total running time: 0h3m1s