[2024-01-25 19:38:50,604] [INFO] DFAST_QC pipeline started. [2024-01-25 19:38:50,605] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:38:50,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference [2024-01-25 19:38:51,754] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:38:51,754] [INFO] Task started: Prodigal [2024-01-25 19:38:51,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bf5743f-91ec-41de-9510-c4691ef8cd68/GCF_902499165.1_ASM90249916v1_genomic.fna.gz | prodigal -d GCF_902499165.1_ASM90249916v1_genomic.fna/cds.fna -a GCF_902499165.1_ASM90249916v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:39:12,333] [INFO] Task succeeded: Prodigal [2024-01-25 19:39:12,333] [INFO] Task started: HMMsearch [2024-01-25 19:39:12,333] [INFO] Running command: hmmsearch --tblout GCF_902499165.1_ASM90249916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/reference_markers.hmm GCF_902499165.1_ASM90249916v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:39:12,641] [INFO] Task succeeded: HMMsearch [2024-01-25 19:39:12,642] [INFO] Found 6/6 markers. [2024-01-25 19:39:12,698] [INFO] Query marker FASTA was written to GCF_902499165.1_ASM90249916v1_genomic.fna/markers.fasta [2024-01-25 19:39:12,698] [INFO] Task started: Blastn [2024-01-25 19:39:12,698] [INFO] Running command: blastn -query GCF_902499165.1_ASM90249916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/reference_markers.fasta -out GCF_902499165.1_ASM90249916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:39:13,698] [INFO] Task succeeded: Blastn [2024-01-25 19:39:13,701] [INFO] Selected 18 target genomes. [2024-01-25 19:39:13,701] [INFO] Target genome list was writen to GCF_902499165.1_ASM90249916v1_genomic.fna/target_genomes.txt [2024-01-25 19:39:13,713] [INFO] Task started: fastANI [2024-01-25 19:39:13,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf5743f-91ec-41de-9510-c4691ef8cd68/GCF_902499165.1_ASM90249916v1_genomic.fna.gz --refList GCF_902499165.1_ASM90249916v1_genomic.fna/target_genomes.txt --output GCF_902499165.1_ASM90249916v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:39:52,227] [INFO] Task succeeded: fastANI [2024-01-25 19:39:52,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:39:52,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:39:52,239] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold) [2024-01-25 19:39:52,240] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:39:52,240] [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 GCA_902499165.1 488731 488731 type True 100.0 2547 2556 95 conclusive Burkholderia seminalis strain=LMG 24067 GCA_902832885.1 488731 488731 type True 99.9975 2550 2556 95 conclusive Burkholderia arboris GCA_902499125.1 488730 488730 type True 93.4603 1981 2556 95 below_threshold Burkholderia pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 92.6857 1951 2556 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 92.6223 1975 2556 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 92.2854 2088 2556 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 92.2475 2070 2556 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 92.156 2017 2556 95 below_threshold Burkholderia lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 92.0794 1951 2556 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 91.9546 2139 2556 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 91.9377 2124 2556 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.7708 1807 2556 95 below_threshold Burkholderia anthina strain=LMG 20980 GCA_902830395.1 179879 179879 suspected-type True 90.7616 1828 2556 95 below_threshold Burkholderia anthina GCA_902498995.1 179879 179879 suspected-type True 90.7109 1824 2556 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.7964 1672 2556 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.7331 1702 2556 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.5166 1374 2556 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.0051 1237 2556 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:39:52,241] [INFO] DFAST Taxonomy check result was written to GCF_902499165.1_ASM90249916v1_genomic.fna/tc_result.tsv [2024-01-25 19:39:52,242] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:39:52,242] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:39:52,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/checkm_data [2024-01-25 19:39:52,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:39:52,322] [INFO] Task started: CheckM [2024-01-25 19:39:52,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499165.1_ASM90249916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499165.1_ASM90249916v1_genomic.fna/checkm_input GCF_902499165.1_ASM90249916v1_genomic.fna/checkm_result [2024-01-25 19:41:08,582] [INFO] Task succeeded: CheckM [2024-01-25 19:41:08,583] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:41:08,606] [INFO] ===== Completeness check finished ===== [2024-01-25 19:41:08,606] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:41:08,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499165.1_ASM90249916v1_genomic.fna/markers.fasta) [2024-01-25 19:41:08,608] [INFO] Task started: Blastn [2024-01-25 19:41:08,608] [INFO] Running command: blastn -query GCF_902499165.1_ASM90249916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad96e9dd-d2da-4e54-bf06-fca2eff30791/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499165.1_ASM90249916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:41:10,593] [INFO] Task succeeded: Blastn [2024-01-25 19:41:10,596] [INFO] Selected 15 target genomes. [2024-01-25 19:41:10,596] [INFO] Target genome list was writen to GCF_902499165.1_ASM90249916v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:41:10,624] [INFO] Task started: fastANI [2024-01-25 19:41:10,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf5743f-91ec-41de-9510-c4691ef8cd68/GCF_902499165.1_ASM90249916v1_genomic.fna.gz --refList GCF_902499165.1_ASM90249916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499165.1_ASM90249916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:41:46,554] [INFO] Task succeeded: fastANI [2024-01-25 19:41:46,563] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:41:46,564] [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 99.9975 2550 2556 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_003853705.1 s__Burkholderia sp003853705 93.967 2019 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902833225.1 s__Burkholderia sp902833225 93.9446 2053 2556 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 93.4668 1981 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_900446215.1 s__Burkholderia cenocepacia 92.7009 2003 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - GCF_001028665.1 s__Burkholderia pyrrocinia 92.6237 1974 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.68 95.03 0.81 0.77 21 - GCF_902833145.1 s__Burkholderia sp902833145 92.5525 1924 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_016899425.1 s__Burkholderia sp002223185 92.5171 1996 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_001547525.1 s__Burkholderia anthina_A 92.4636 1941 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.44 98.20 0.94 0.91 13 - GCF_902499335.1 s__Burkholderia lata_B 92.2135 2010 2556 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 92.1006 1949 2556 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 91.9544 2139 2556 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 91.4683 1729 2556 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 91.2367 1657 2556 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 90.4759 1832 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 19:41:46,565] [INFO] GTDB search result was written to GCF_902499165.1_ASM90249916v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:41:46,565] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:41:46,569] [INFO] DFAST_QC result json was written to GCF_902499165.1_ASM90249916v1_genomic.fna/dqc_result.json [2024-01-25 19:41:46,569] [INFO] DFAST_QC completed! [2024-01-25 19:41:46,569] [INFO] Total running time: 0h2m56s