[2024-01-24 13:46:40,765] [INFO] DFAST_QC pipeline started. [2024-01-24 13:46:40,767] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:46:40,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference [2024-01-24 13:46:42,064] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:46:42,065] [INFO] Task started: Prodigal [2024-01-24 13:46:42,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg85b99c60-f730-46ef-b178-d196818e3ec6/GCF_902832895.1_ASM90283289v1_genomic.fna.gz | prodigal -d GCF_902832895.1_ASM90283289v1_genomic.fna/cds.fna -a GCF_902832895.1_ASM90283289v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:47:06,647] [INFO] Task succeeded: Prodigal [2024-01-24 13:47:06,648] [INFO] Task started: HMMsearch [2024-01-24 13:47:06,648] [INFO] Running command: hmmsearch --tblout GCF_902832895.1_ASM90283289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/reference_markers.hmm GCF_902832895.1_ASM90283289v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:47:07,135] [INFO] Task succeeded: HMMsearch [2024-01-24 13:47:07,137] [INFO] Found 6/6 markers. [2024-01-24 13:47:07,200] [INFO] Query marker FASTA was written to GCF_902832895.1_ASM90283289v1_genomic.fna/markers.fasta [2024-01-24 13:47:07,201] [INFO] Task started: Blastn [2024-01-24 13:47:07,201] [INFO] Running command: blastn -query GCF_902832895.1_ASM90283289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/reference_markers.fasta -out GCF_902832895.1_ASM90283289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:47:08,294] [INFO] Task succeeded: Blastn [2024-01-24 13:47:08,298] [INFO] Selected 19 target genomes. [2024-01-24 13:47:08,299] [INFO] Target genome list was writen to GCF_902832895.1_ASM90283289v1_genomic.fna/target_genomes.txt [2024-01-24 13:47:08,302] [INFO] Task started: fastANI [2024-01-24 13:47:08,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b99c60-f730-46ef-b178-d196818e3ec6/GCF_902832895.1_ASM90283289v1_genomic.fna.gz --refList GCF_902832895.1_ASM90283289v1_genomic.fna/target_genomes.txt --output GCF_902832895.1_ASM90283289v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:47:51,746] [INFO] Task succeeded: fastANI [2024-01-24 13:47:51,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:47:51,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:47:51,770] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:47:51,770] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:47:51,770] [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 pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 100.0 2600 2601 95 conclusive Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 99.9977 2601 2601 95 conclusive Burkholderia catarinensis strain=89 GCA_001883705.2 1108140 1108140 type True 93.3887 2074 2601 95 below_threshold Burkholderia stabilis strain=ATCC BAA-67 GCA_001742165.1 95485 95485 type True 93.2354 2005 2601 95 below_threshold Burkholderia arboris GCA_902499125.1 488730 488730 type True 92.8243 2040 2601 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 92.7934 2120 2601 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 92.7916 2089 2601 95 below_threshold Burkholderia cepacia strain=UCB 717 GCA_001411495.1 292 292 type True 92.7809 2122 2601 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 92.7599 2059 2601 95 below_threshold Burkholderia puraquae strain=LMG 29660 GCA_902859845.1 1904757 1904757 type True 92.7202 2060 2601 95 below_threshold Burkholderia metallica strain=LMG 24068 GCA_902832845.1 488729 488729 type True 92.3892 1973 2601 95 below_threshold Burkholderia metallica GCA_902499065.1 488729 488729 type True 92.3681 1939 2601 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 92.2272 2110 2601 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 92.226 2106 2601 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 91.0158 1857 2601 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 89.14 1814 2601 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 89.0679 1749 2601 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.6979 1369 2601 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.1441 1233 2601 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:47:51,772] [INFO] DFAST Taxonomy check result was written to GCF_902832895.1_ASM90283289v1_genomic.fna/tc_result.tsv [2024-01-24 13:47:51,773] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:47:51,773] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:47:51,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/checkm_data [2024-01-24 13:47:51,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:47:51,856] [INFO] Task started: CheckM [2024-01-24 13:47:51,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902832895.1_ASM90283289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902832895.1_ASM90283289v1_genomic.fna/checkm_input GCF_902832895.1_ASM90283289v1_genomic.fna/checkm_result [2024-01-24 13:49:05,847] [INFO] Task succeeded: CheckM [2024-01-24 13:49:05,849] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:49:05,881] [INFO] ===== Completeness check finished ===== [2024-01-24 13:49:05,881] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:49:05,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902832895.1_ASM90283289v1_genomic.fna/markers.fasta) [2024-01-24 13:49:05,882] [INFO] Task started: Blastn [2024-01-24 13:49:05,882] [INFO] Running command: blastn -query GCF_902832895.1_ASM90283289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg638ffa0e-64bd-404a-b19c-51afe02cf8c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_902832895.1_ASM90283289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:49:08,029] [INFO] Task succeeded: Blastn [2024-01-24 13:49:08,033] [INFO] Selected 19 target genomes. [2024-01-24 13:49:08,034] [INFO] Target genome list was writen to GCF_902832895.1_ASM90283289v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:49:08,051] [INFO] Task started: fastANI [2024-01-24 13:49:08,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b99c60-f730-46ef-b178-d196818e3ec6/GCF_902832895.1_ASM90283289v1_genomic.fna.gz --refList GCF_902832895.1_ASM90283289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902832895.1_ASM90283289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:49:52,392] [INFO] Task succeeded: fastANI [2024-01-24 13:49:52,410] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:49:52,410] [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_001028665.1 s__Burkholderia pyrrocinia 99.9977 2601 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.68 95.03 0.81 0.77 21 conclusive GCF_001039005.1 s__Burkholderia cepacia_C 93.8886 2121 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.16 97.10 0.89 0.88 3 - GCF_003330765.1 s__Burkholderia pyrrocinia_B 93.6684 2029 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001742165.1 s__Burkholderia stabilis 93.2575 2002 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.17 98.56 0.94 0.88 6 - GCA_001883705.1 s__Burkholderia catarinensis 93.1347 1755 2601 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 92.843 2038 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_902833225.1 s__Burkholderia sp902833225 92.8404 2064 2601 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 92.7758 2122 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.84 96.33 0.89 0.79 182 - GCF_002099195.1 s__Burkholderia puraquae 92.7609 2059 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.50 95.00 0.89 0.80 3 - GCF_902832885.1 s__Burkholderia seminalis 92.7121 2024 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.92 97.02 0.94 0.87 12 - GCF_902499335.1 s__Burkholderia lata_B 92.7105 2101 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.27 95.15 0.87 0.83 7 - GCF_003853705.1 s__Burkholderia sp003853705 92.7067 2037 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902833045.1 s__Burkholderia sp902833045 92.5737 1975 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.81 96.81 0.81 0.81 2 - GCF_000987075.1 s__Burkholderia contaminans 92.2088 2107 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_016899425.1 s__Burkholderia sp002223185 92.0304 2007 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_000732615.1 s__Burkholderia paludis 91.9765 1896 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.34 99.33 0.95 0.95 4 - GCF_001718835.1 s__Burkholderia cepacia_F 91.8731 1820 2601 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 91.7102 1742 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001443045.1 s__Burkholderia ambifaria_A 91.123 1875 2601 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - -------------------------------------------------------------------------------- [2024-01-24 13:49:52,412] [INFO] GTDB search result was written to GCF_902832895.1_ASM90283289v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:49:52,413] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:49:52,418] [INFO] DFAST_QC result json was written to GCF_902832895.1_ASM90283289v1_genomic.fna/dqc_result.json [2024-01-24 13:49:52,418] [INFO] DFAST_QC completed! [2024-01-24 13:49:52,418] [INFO] Total running time: 0h3m12s