[2024-01-24 14:03:03,552] [INFO] DFAST_QC pipeline started. [2024-01-24 14:03:03,554] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:03:03,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference [2024-01-24 14:03:04,787] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:03:04,788] [INFO] Task started: Prodigal [2024-01-24 14:03:04,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a669129-6ce7-4f34-9d04-2bd6682f0852/GCF_902832845.1_ASM90283284v1_genomic.fna.gz | prodigal -d GCF_902832845.1_ASM90283284v1_genomic.fna/cds.fna -a GCF_902832845.1_ASM90283284v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:03:27,797] [INFO] Task succeeded: Prodigal [2024-01-24 14:03:27,798] [INFO] Task started: HMMsearch [2024-01-24 14:03:27,798] [INFO] Running command: hmmsearch --tblout GCF_902832845.1_ASM90283284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/reference_markers.hmm GCF_902832845.1_ASM90283284v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:03:28,181] [INFO] Task succeeded: HMMsearch [2024-01-24 14:03:28,183] [INFO] Found 6/6 markers. [2024-01-24 14:03:28,241] [INFO] Query marker FASTA was written to GCF_902832845.1_ASM90283284v1_genomic.fna/markers.fasta [2024-01-24 14:03:28,242] [INFO] Task started: Blastn [2024-01-24 14:03:28,242] [INFO] Running command: blastn -query GCF_902832845.1_ASM90283284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/reference_markers.fasta -out GCF_902832845.1_ASM90283284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:03:29,383] [INFO] Task succeeded: Blastn [2024-01-24 14:03:29,386] [INFO] Selected 17 target genomes. [2024-01-24 14:03:29,387] [INFO] Target genome list was writen to GCF_902832845.1_ASM90283284v1_genomic.fna/target_genomes.txt [2024-01-24 14:03:29,395] [INFO] Task started: fastANI [2024-01-24 14:03:29,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a669129-6ce7-4f34-9d04-2bd6682f0852/GCF_902832845.1_ASM90283284v1_genomic.fna.gz --refList GCF_902832845.1_ASM90283284v1_genomic.fna/target_genomes.txt --output GCF_902832845.1_ASM90283284v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:04:08,450] [INFO] Task succeeded: fastANI [2024-01-24 14:04:08,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:04:08,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:04:08,464] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold) [2024-01-24 14:04:08,464] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:04:08,464] [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 metallica strain=LMG 24068 GCA_902832845.1 488729 488729 type True 100.0 2501 2502 95 conclusive Burkholderia metallica GCA_902499065.1 488729 488729 type True 99.975 2434 2502 95 conclusive Burkholderia lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 93.3218 2058 2502 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 93.1512 2080 2502 95 below_threshold Burkholderia puraquae strain=LMG 29660 GCA_902859845.1 1904757 1904757 type True 93.1511 2068 2502 95 below_threshold Burkholderia aenigmatica strain=LMG 13014 GCA_902499175.1 2015348 2015348 suspected-type True 93.0377 1964 2502 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 93.0288 2072 2502 95 below_threshold Burkholderia cepacia strain=UCB 717 GCA_001411495.1 292 292 type True 93.0267 2082 2502 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 93.0265 2127 2502 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 93.0186 2055 2502 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 92.978 2106 2502 95 below_threshold Burkholderia cenocepacia strain=NCTC13227 GCA_900446215.1 95486 95486 type True 92.2113 2015 2502 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.6777 1861 2502 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.7488 1713 2502 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.7302 1677 2502 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.4974 1377 2502 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.2141 1245 2502 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:04:08,466] [INFO] DFAST Taxonomy check result was written to GCF_902832845.1_ASM90283284v1_genomic.fna/tc_result.tsv [2024-01-24 14:04:08,466] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:04:08,466] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:04:08,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/checkm_data [2024-01-24 14:04:08,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:04:08,544] [INFO] Task started: CheckM [2024-01-24 14:04:08,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902832845.1_ASM90283284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902832845.1_ASM90283284v1_genomic.fna/checkm_input GCF_902832845.1_ASM90283284v1_genomic.fna/checkm_result [2024-01-24 14:05:21,252] [INFO] Task succeeded: CheckM [2024-01-24 14:05:21,254] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:05:21,279] [INFO] ===== Completeness check finished ===== [2024-01-24 14:05:21,279] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:05:21,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902832845.1_ASM90283284v1_genomic.fna/markers.fasta) [2024-01-24 14:05:21,280] [INFO] Task started: Blastn [2024-01-24 14:05:21,280] [INFO] Running command: blastn -query GCF_902832845.1_ASM90283284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg138f64c7-d321-484d-b530-5d43d8578622/dqc_reference/reference_markers_gtdb.fasta -out GCF_902832845.1_ASM90283284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:05:23,372] [INFO] Task succeeded: Blastn [2024-01-24 14:05:23,376] [INFO] Selected 16 target genomes. [2024-01-24 14:05:23,376] [INFO] Target genome list was writen to GCF_902832845.1_ASM90283284v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:05:23,392] [INFO] Task started: fastANI [2024-01-24 14:05:23,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a669129-6ce7-4f34-9d04-2bd6682f0852/GCF_902832845.1_ASM90283284v1_genomic.fna.gz --refList GCF_902832845.1_ASM90283284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902832845.1_ASM90283284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:05:59,498] [INFO] Task succeeded: fastANI [2024-01-24 14:05:59,518] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:05:59,519] [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_902832845.1 s__Burkholderia metallica 100.0 2501 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.19 98.00 0.94 0.86 6 conclusive GCF_000012945.1 s__Burkholderia lata 93.325 2057 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.30 0.88 0.82 11 - GCF_902499335.1 s__Burkholderia lata_B 93.3194 2078 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.27 95.15 0.87 0.83 7 - GCF_902833045.1 s__Burkholderia sp902833045 93.3069 1969 2502 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 93.151 2081 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.50 95.00 0.89 0.80 3 - GCF_000987075.1 s__Burkholderia contaminans 93.0527 2124 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_902499175.1 s__Burkholderia aenigmatica 93.0343 1965 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.89 95.59 0.85 0.80 12 - GCF_001411495.1 s__Burkholderia cepacia 92.9992 2085 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.84 96.33 0.89 0.79 182 - GCF_900446215.1 s__Burkholderia cenocepacia 92.1815 2020 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - GCF_001718835.1 s__Burkholderia cepacia_F 92.106 1739 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902833145.1 s__Burkholderia sp902833145 92.0004 1900 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_001522585.2 s__Burkholderia sp001522585 91.9688 1933 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.44 95.03 0.88 0.83 18 - GCF_016899425.1 s__Burkholderia sp002223185 91.9503 1928 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_014211915.1 s__Burkholderia cenocepacia_B 91.9453 2010 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 97.84 96.64 0.90 0.85 89 - GCF_000732615.1 s__Burkholderia paludis 91.7591 1880 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.34 99.33 0.95 0.95 4 - GCF_000949135.2 s__Burkholderia sp000949135 91.0211 1879 2502 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - -------------------------------------------------------------------------------- [2024-01-24 14:05:59,521] [INFO] GTDB search result was written to GCF_902832845.1_ASM90283284v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:05:59,521] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:05:59,525] [INFO] DFAST_QC result json was written to GCF_902832845.1_ASM90283284v1_genomic.fna/dqc_result.json [2024-01-24 14:05:59,525] [INFO] DFAST_QC completed! [2024-01-24 14:05:59,525] [INFO] Total running time: 0h2m56s