[2024-01-24 13:13:39,321] [INFO] DFAST_QC pipeline started. [2024-01-24 13:13:39,324] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:13:39,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference [2024-01-24 13:13:40,665] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:13:40,666] [INFO] Task started: Prodigal [2024-01-24 13:13:40,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg2792f5f2-7e21-4034-96d5-15767a6160f8/GCF_900446205.1_51485_A01_genomic.fna.gz | prodigal -d GCF_900446205.1_51485_A01_genomic.fna/cds.fna -a GCF_900446205.1_51485_A01_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:13:59,909] [INFO] Task succeeded: Prodigal [2024-01-24 13:13:59,909] [INFO] Task started: HMMsearch [2024-01-24 13:13:59,909] [INFO] Running command: hmmsearch --tblout GCF_900446205.1_51485_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/reference_markers.hmm GCF_900446205.1_51485_A01_genomic.fna/protein.faa > /dev/null [2024-01-24 13:14:00,252] [INFO] Task succeeded: HMMsearch [2024-01-24 13:14:00,253] [INFO] Found 6/6 markers. [2024-01-24 13:14:00,305] [INFO] Query marker FASTA was written to GCF_900446205.1_51485_A01_genomic.fna/markers.fasta [2024-01-24 13:14:00,305] [INFO] Task started: Blastn [2024-01-24 13:14:00,305] [INFO] Running command: blastn -query GCF_900446205.1_51485_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/reference_markers.fasta -out GCF_900446205.1_51485_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:14:01,382] [INFO] Task succeeded: Blastn [2024-01-24 13:14:01,387] [INFO] Selected 15 target genomes. [2024-01-24 13:14:01,388] [INFO] Target genome list was writen to GCF_900446205.1_51485_A01_genomic.fna/target_genomes.txt [2024-01-24 13:14:01,393] [INFO] Task started: fastANI [2024-01-24 13:14:01,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg2792f5f2-7e21-4034-96d5-15767a6160f8/GCF_900446205.1_51485_A01_genomic.fna.gz --refList GCF_900446205.1_51485_A01_genomic.fna/target_genomes.txt --output GCF_900446205.1_51485_A01_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:14:30,514] [INFO] Task succeeded: fastANI [2024-01-24 13:14:30,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:14:30,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:14:30,529] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold) [2024-01-24 13:14:30,530] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:14:30,530] [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 multivorans strain=NCTC13007 GCA_900446205.1 87883 87883 type True 100.0 2099 2099 95 conclusive Burkholderia multivorans strain=ATCC BAA-247 GCA_000959525.1 87883 87883 type True 99.9985 2095 2099 95 conclusive Burkholderia multivorans strain=ATCC BAA-247 GCA_000286555.1 87883 87883 type True 99.7573 1743 2099 95 conclusive Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 91.0377 1699 2099 95 below_threshold Burkholderia dolosa strain=LMG 18943 GCA_902499135.1 152500 152500 type True 89.6685 1501 2099 95 below_threshold Burkholderia cenocepacia strain=NCTC13227 GCA_900446215.1 95486 95486 type True 89.3875 1697 2099 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 89.3797 1611 2099 95 below_threshold Burkholderia metallica strain=LMG 24068 GCA_902832845.1 488729 488729 type True 89.2129 1662 2099 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 89.1891 1610 2099 95 below_threshold Burkholderia metallica GCA_902499065.1 488729 488729 type True 89.1366 1614 2099 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 89.1297 1679 2099 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.2164 1488 2099 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.1356 1539 2099 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7902 1295 2099 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 82.05 1082 2099 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:14:30,533] [INFO] DFAST Taxonomy check result was written to GCF_900446205.1_51485_A01_genomic.fna/tc_result.tsv [2024-01-24 13:14:30,534] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:14:30,534] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:14:30,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/checkm_data [2024-01-24 13:14:30,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:14:30,603] [INFO] Task started: CheckM [2024-01-24 13:14:30,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446205.1_51485_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446205.1_51485_A01_genomic.fna/checkm_input GCF_900446205.1_51485_A01_genomic.fna/checkm_result [2024-01-24 13:15:25,471] [INFO] Task succeeded: CheckM [2024-01-24 13:15:25,472] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:15:25,492] [INFO] ===== Completeness check finished ===== [2024-01-24 13:15:25,492] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:15:25,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446205.1_51485_A01_genomic.fna/markers.fasta) [2024-01-24 13:15:25,493] [INFO] Task started: Blastn [2024-01-24 13:15:25,493] [INFO] Running command: blastn -query GCF_900446205.1_51485_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e18925d-0b6c-4985-8b0f-8cfbde815765/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446205.1_51485_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:15:27,645] [INFO] Task succeeded: Blastn [2024-01-24 13:15:27,649] [INFO] Selected 17 target genomes. [2024-01-24 13:15:27,649] [INFO] Target genome list was writen to GCF_900446205.1_51485_A01_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:15:27,673] [INFO] Task started: fastANI [2024-01-24 13:15:27,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg2792f5f2-7e21-4034-96d5-15767a6160f8/GCF_900446205.1_51485_A01_genomic.fna.gz --refList GCF_900446205.1_51485_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446205.1_51485_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:16:01,615] [INFO] Task succeeded: fastANI [2024-01-24 13:16:01,629] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:16:01,629] [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_000959525.1 s__Burkholderia multivorans 99.9985 2095 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.58 96.90 0.90 0.85 326 conclusive GCF_902499075.1 s__Burkholderia pseudomultivorans 91.0182 1701 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_902499135.1 s__Burkholderia dolosa 89.6585 1502 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.52 98.66 0.97 0.91 15 - GCF_900446215.1 s__Burkholderia cenocepacia 89.3855 1699 2099 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 89.3849 1611 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.68 95.03 0.81 0.77 21 - GCF_001522585.2 s__Burkholderia sp001522585 89.3491 1677 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.44 95.03 0.88 0.83 18 - GCF_000949135.2 s__Burkholderia sp000949135 89.3439 1668 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_902499045.1 s__Burkholderia latens 89.3019 1628 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_902832845.1 s__Burkholderia metallica 89.2378 1659 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.19 98.00 0.94 0.86 6 - GCF_016899425.1 s__Burkholderia sp002223185 89.2266 1676 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_003853645.1 s__Burkholderia sp003853645 89.0368 1613 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_001443045.1 s__Burkholderia ambifaria_A 89.0189 1616 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_001718835.1 s__Burkholderia cepacia_F 88.768 1544 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000732615.1 s__Burkholderia paludis 88.7447 1551 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.34 99.33 0.95 0.95 4 - GCF_000959445.1 s__Burkholderia vietnamiensis 88.6911 1563 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.93 97.91 0.90 0.83 111 - GCF_001718795.1 s__Burkholderia latens_A 88.5848 1622 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.33 99.18 0.94 0.92 8 - GCF_003854275.1 s__Burkholderia sp003854275 88.0753 1459 2099 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - -------------------------------------------------------------------------------- [2024-01-24 13:16:01,630] [INFO] GTDB search result was written to GCF_900446205.1_51485_A01_genomic.fna/result_gtdb.tsv [2024-01-24 13:16:01,631] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:16:01,635] [INFO] DFAST_QC result json was written to GCF_900446205.1_51485_A01_genomic.fna/dqc_result.json [2024-01-24 13:16:01,635] [INFO] DFAST_QC completed! [2024-01-24 13:16:01,635] [INFO] Total running time: 0h2m22s