[2024-01-24 13:28:25,947] [INFO] DFAST_QC pipeline started. [2024-01-24 13:28:25,950] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:28:25,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference [2024-01-24 13:28:27,301] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:28:27,305] [INFO] Task started: Prodigal [2024-01-24 13:28:27,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg97a0560d-3234-49fc-9aef-26f7b2c2bc45/GCF_902499035.1_ASM90249903v1_genomic.fna.gz | prodigal -d GCF_902499035.1_ASM90249903v1_genomic.fna/cds.fna -a GCF_902499035.1_ASM90249903v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:28:49,078] [INFO] Task succeeded: Prodigal [2024-01-24 13:28:49,078] [INFO] Task started: HMMsearch [2024-01-24 13:28:49,078] [INFO] Running command: hmmsearch --tblout GCF_902499035.1_ASM90249903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/reference_markers.hmm GCF_902499035.1_ASM90249903v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:28:49,508] [INFO] Task succeeded: HMMsearch [2024-01-24 13:28:49,509] [INFO] Found 6/6 markers. [2024-01-24 13:28:49,564] [INFO] Query marker FASTA was written to GCF_902499035.1_ASM90249903v1_genomic.fna/markers.fasta [2024-01-24 13:28:49,564] [INFO] Task started: Blastn [2024-01-24 13:28:49,564] [INFO] Running command: blastn -query GCF_902499035.1_ASM90249903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/reference_markers.fasta -out GCF_902499035.1_ASM90249903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:28:50,564] [INFO] Task succeeded: Blastn [2024-01-24 13:28:50,568] [INFO] Selected 15 target genomes. [2024-01-24 13:28:50,569] [INFO] Target genome list was writen to GCF_902499035.1_ASM90249903v1_genomic.fna/target_genomes.txt [2024-01-24 13:28:50,583] [INFO] Task started: fastANI [2024-01-24 13:28:50,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg97a0560d-3234-49fc-9aef-26f7b2c2bc45/GCF_902499035.1_ASM90249903v1_genomic.fna.gz --refList GCF_902499035.1_ASM90249903v1_genomic.fna/target_genomes.txt --output GCF_902499035.1_ASM90249903v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:29:19,441] [INFO] Task succeeded: fastANI [2024-01-24 13:29:19,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:29:19,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:29:19,458] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold) [2024-01-24 13:29:19,459] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:29:19,459] [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 territorii GCA_902499035.1 1503055 1503055 type True 100.0 2248 2251 95 conclusive Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 99.9941 2227 2251 95 conclusive Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 99.5949 1558 2251 95 conclusive Burkholderia diffusa GCA_902499115.1 488732 488732 suspected-type True 93.8597 1823 2251 95 below_threshold Burkholderia diffusa strain=DSM 23434 GCA_016836765.1 488732 488732 suspected-type True 93.8538 1837 2251 95 below_threshold Burkholderia diffusa strain=CCUG 54558 GCA_008802145.1 488732 488732 suspected-type True 93.8362 1660 2251 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000959545.1 152480 152480 type True 92.1631 1826 2251 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 92.133 1834 2251 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 91.6219 1749 2251 95 below_threshold Burkholderia arboris GCA_902499125.1 488730 488730 type True 90.4655 1744 2251 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 90.1038 1647 2251 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.4721 1608 2251 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.4018 1647 2251 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.605 1272 2251 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.1209 1164 2251 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:29:19,461] [INFO] DFAST Taxonomy check result was written to GCF_902499035.1_ASM90249903v1_genomic.fna/tc_result.tsv [2024-01-24 13:29:19,462] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:29:19,462] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:29:19,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/checkm_data [2024-01-24 13:29:19,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:29:19,541] [INFO] Task started: CheckM [2024-01-24 13:29:19,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499035.1_ASM90249903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499035.1_ASM90249903v1_genomic.fna/checkm_input GCF_902499035.1_ASM90249903v1_genomic.fna/checkm_result [2024-01-24 13:30:29,424] [INFO] Task succeeded: CheckM [2024-01-24 13:30:29,426] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:30:29,450] [INFO] ===== Completeness check finished ===== [2024-01-24 13:30:29,451] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:30:29,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499035.1_ASM90249903v1_genomic.fna/markers.fasta) [2024-01-24 13:30:29,451] [INFO] Task started: Blastn [2024-01-24 13:30:29,452] [INFO] Running command: blastn -query GCF_902499035.1_ASM90249903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e79c7b-adbb-4bb0-8b36-3cc4e0ebacf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499035.1_ASM90249903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:30:31,128] [INFO] Task succeeded: Blastn [2024-01-24 13:30:31,132] [INFO] Selected 11 target genomes. [2024-01-24 13:30:31,132] [INFO] Target genome list was writen to GCF_902499035.1_ASM90249903v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:30:31,143] [INFO] Task started: fastANI [2024-01-24 13:30:31,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg97a0560d-3234-49fc-9aef-26f7b2c2bc45/GCF_902499035.1_ASM90249903v1_genomic.fna.gz --refList GCF_902499035.1_ASM90249903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499035.1_ASM90249903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:30:53,446] [INFO] Task succeeded: fastANI [2024-01-24 13:30:53,465] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:30:53,466] [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_902833055.1 s__Burkholderia territorii 99.9941 2227 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 conclusive GCF_001718315.1 s__Burkholderia diffusa_B 95.0476 1920 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.43 98.33 0.91 0.89 12 - GCF_902499115.1 s__Burkholderia diffusa 93.8704 1822 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 - GCF_000949135.2 s__Burkholderia sp000949135 93.2414 1868 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_003853645.1 s__Burkholderia sp003853645 93.1307 1783 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_003853415.1 s__Burkholderia sp003853415 92.6903 1823 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_001443045.1 s__Burkholderia ambifaria_A 92.4194 1755 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_001547525.1 s__Burkholderia anthina_A 90.5081 1782 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.44 98.20 0.94 0.91 13 - GCF_902499125.1 s__Burkholderia arboris 90.4657 1744 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_014211915.1 s__Burkholderia cenocepacia_B 90.3427 1828 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 97.84 96.64 0.90 0.85 89 - GCF_902499075.1 s__Burkholderia pseudomultivorans 90.1015 1647 2251 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - -------------------------------------------------------------------------------- [2024-01-24 13:30:53,468] [INFO] GTDB search result was written to GCF_902499035.1_ASM90249903v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:30:53,469] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:30:53,477] [INFO] DFAST_QC result json was written to GCF_902499035.1_ASM90249903v1_genomic.fna/dqc_result.json [2024-01-24 13:30:53,477] [INFO] DFAST_QC completed! [2024-01-24 13:30:53,477] [INFO] Total running time: 0h2m28s