[2024-01-24 12:43:54,223] [INFO] DFAST_QC pipeline started. [2024-01-24 12:43:54,225] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:43:54,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference [2024-01-24 12:43:59,334] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:43:59,335] [INFO] Task started: Prodigal [2024-01-24 12:43:59,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cdd4de6-587f-4168-8bf2-90529166250c/GCF_001883705.2_ASM188370v2_genomic.fna.gz | prodigal -d GCF_001883705.2_ASM188370v2_genomic.fna/cds.fna -a GCF_001883705.2_ASM188370v2_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:44:24,504] [INFO] Task succeeded: Prodigal [2024-01-24 12:44:24,504] [INFO] Task started: HMMsearch [2024-01-24 12:44:24,504] [INFO] Running command: hmmsearch --tblout GCF_001883705.2_ASM188370v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/reference_markers.hmm GCF_001883705.2_ASM188370v2_genomic.fna/protein.faa > /dev/null [2024-01-24 12:44:24,871] [INFO] Task succeeded: HMMsearch [2024-01-24 12:44:24,873] [INFO] Found 6/6 markers. [2024-01-24 12:44:24,939] [INFO] Query marker FASTA was written to GCF_001883705.2_ASM188370v2_genomic.fna/markers.fasta [2024-01-24 12:44:24,940] [INFO] Task started: Blastn [2024-01-24 12:44:24,940] [INFO] Running command: blastn -query GCF_001883705.2_ASM188370v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/reference_markers.fasta -out GCF_001883705.2_ASM188370v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:44:25,989] [INFO] Task succeeded: Blastn [2024-01-24 12:44:25,993] [INFO] Selected 19 target genomes. [2024-01-24 12:44:25,994] [INFO] Target genome list was writen to GCF_001883705.2_ASM188370v2_genomic.fna/target_genomes.txt [2024-01-24 12:44:26,019] [INFO] Task started: fastANI [2024-01-24 12:44:26,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cdd4de6-587f-4168-8bf2-90529166250c/GCF_001883705.2_ASM188370v2_genomic.fna.gz --refList GCF_001883705.2_ASM188370v2_genomic.fna/target_genomes.txt --output GCF_001883705.2_ASM188370v2_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:45:08,668] [INFO] Task succeeded: fastANI [2024-01-24 12:45:08,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:45:08,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:45:08,683] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold) [2024-01-24 12:45:08,684] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:45:08,684] [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 catarinensis strain=89 GCA_001883705.2 1108140 1108140 type True 100.0 2690 2694 95 conclusive Burkholderia pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 93.4445 2086 2694 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 93.4282 2086 2694 95 below_threshold Burkholderia arboris GCA_902499125.1 488730 488730 type True 92.87 2054 2694 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 92.859 2119 2694 95 below_threshold Burkholderia puraquae strain=LMG 29660 GCA_902859845.1 1904757 1904757 type True 92.8374 2113 2694 95 below_threshold Burkholderia aenigmatica strain=LMG 13014 GCA_902499175.1 2015348 2015348 suspected-type True 92.7804 1979 2694 95 below_threshold Burkholderia lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 92.6881 2113 2694 95 below_threshold Burkholderia seminalis strain=LMG 24067 GCA_902832885.1 488731 488731 type True 92.5261 2016 2694 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 92.5238 2141 2694 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 92.4469 2151 2694 95 below_threshold Burkholderia paludis strain=MSh1 GCA_000732615.1 1506587 1506587 type True 91.9786 1932 2694 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 91.0865 1885 2694 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 88.9488 1817 2694 95 below_threshold Burkholderia stagnalis GCA_902499155.1 1503054 1503054 type True 88.8855 1752 2694 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.8339 1775 2694 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.7941 1843 2694 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.3207 1400 2694 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.9589 1267 2694 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:45:08,695] [INFO] DFAST Taxonomy check result was written to GCF_001883705.2_ASM188370v2_genomic.fna/tc_result.tsv [2024-01-24 12:45:08,696] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:45:08,696] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:45:08,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/checkm_data [2024-01-24 12:45:08,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:45:08,792] [INFO] Task started: CheckM [2024-01-24 12:45:08,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001883705.2_ASM188370v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001883705.2_ASM188370v2_genomic.fna/checkm_input GCF_001883705.2_ASM188370v2_genomic.fna/checkm_result [2024-01-24 12:46:28,998] [INFO] Task succeeded: CheckM [2024-01-24 12:46:28,999] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:46:29,025] [INFO] ===== Completeness check finished ===== [2024-01-24 12:46:29,025] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:46:29,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001883705.2_ASM188370v2_genomic.fna/markers.fasta) [2024-01-24 12:46:29,026] [INFO] Task started: Blastn [2024-01-24 12:46:29,026] [INFO] Running command: blastn -query GCF_001883705.2_ASM188370v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce752f2-d6b9-4cf5-aceb-1e583d9c7a56/dqc_reference/reference_markers_gtdb.fasta -out GCF_001883705.2_ASM188370v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:46:31,056] [INFO] Task succeeded: Blastn [2024-01-24 12:46:31,061] [INFO] Selected 17 target genomes. [2024-01-24 12:46:31,061] [INFO] Target genome list was writen to GCF_001883705.2_ASM188370v2_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:46:31,092] [INFO] Task started: fastANI [2024-01-24 12:46:31,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cdd4de6-587f-4168-8bf2-90529166250c/GCF_001883705.2_ASM188370v2_genomic.fna.gz --refList GCF_001883705.2_ASM188370v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001883705.2_ASM188370v2_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:47:10,682] [INFO] Task succeeded: fastANI [2024-01-24 12:47:10,705] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:47:10,705] [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 GCA_001883705.1 s__Burkholderia catarinensis 99.747 2263 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 conclusive GCF_001028665.1 s__Burkholderia pyrrocinia 93.4422 2084 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.68 95.03 0.81 0.77 21 - GCF_003330765.1 s__Burkholderia pyrrocinia_B 93.4348 2073 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001039005.1 s__Burkholderia cepacia_C 93.1858 2119 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.16 97.10 0.89 0.88 3 - GCF_902833225.1 s__Burkholderia sp902833225 92.9195 2081 2694 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 92.8765 2054 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_902499335.1 s__Burkholderia lata_B 92.847 2150 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.27 95.15 0.87 0.83 7 - GCF_902499175.1 s__Burkholderia aenigmatica 92.8068 1976 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.89 95.59 0.85 0.80 12 - GCF_003853705.1 s__Burkholderia sp003853705 92.766 2049 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_011605345.1 s__Burkholderia sp011605345 92.7132 2101 2694 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 92.7067 2039 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.17 98.56 0.94 0.88 6 - GCF_000012945.1 s__Burkholderia lata 92.6937 2112 2694 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 92.5057 2144 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_000732615.1 s__Burkholderia paludis 91.9988 1930 2694 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 91.7941 1860 2694 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902830275.1 s__Burkholderia stagnalis 88.9541 1818 2694 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 88.9004 1881 2694 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 12:47:10,707] [INFO] GTDB search result was written to GCF_001883705.2_ASM188370v2_genomic.fna/result_gtdb.tsv [2024-01-24 12:47:10,707] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:47:10,712] [INFO] DFAST_QC result json was written to GCF_001883705.2_ASM188370v2_genomic.fna/dqc_result.json [2024-01-24 12:47:10,712] [INFO] DFAST_QC completed! [2024-01-24 12:47:10,712] [INFO] Total running time: 0h3m16s