[2024-01-24 13:57:57,770] [INFO] DFAST_QC pipeline started. [2024-01-24 13:57:57,771] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:57:57,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference [2024-01-24 13:57:59,116] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:57:59,117] [INFO] Task started: Prodigal [2024-01-24 13:57:59,118] [INFO] Running command: gunzip -c /var/lib/cwl/stgce4e205e-7828-439a-b203-0ae90b82021b/GCF_019930785.1_ASM1993078v1_genomic.fna.gz | prodigal -d GCF_019930785.1_ASM1993078v1_genomic.fna/cds.fna -a GCF_019930785.1_ASM1993078v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:58:18,457] [INFO] Task succeeded: Prodigal [2024-01-24 13:58:18,458] [INFO] Task started: HMMsearch [2024-01-24 13:58:18,458] [INFO] Running command: hmmsearch --tblout GCF_019930785.1_ASM1993078v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/reference_markers.hmm GCF_019930785.1_ASM1993078v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:58:18,802] [INFO] Task succeeded: HMMsearch [2024-01-24 13:58:18,804] [INFO] Found 6/6 markers. [2024-01-24 13:58:18,856] [INFO] Query marker FASTA was written to GCF_019930785.1_ASM1993078v1_genomic.fna/markers.fasta [2024-01-24 13:58:18,857] [INFO] Task started: Blastn [2024-01-24 13:58:18,857] [INFO] Running command: blastn -query GCF_019930785.1_ASM1993078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/reference_markers.fasta -out GCF_019930785.1_ASM1993078v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:58:19,989] [INFO] Task succeeded: Blastn [2024-01-24 13:58:19,992] [INFO] Selected 24 target genomes. [2024-01-24 13:58:19,992] [INFO] Target genome list was writen to GCF_019930785.1_ASM1993078v1_genomic.fna/target_genomes.txt [2024-01-24 13:58:20,073] [INFO] Task started: fastANI [2024-01-24 13:58:20,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4e205e-7828-439a-b203-0ae90b82021b/GCF_019930785.1_ASM1993078v1_genomic.fna.gz --refList GCF_019930785.1_ASM1993078v1_genomic.fna/target_genomes.txt --output GCF_019930785.1_ASM1993078v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:59:06,688] [INFO] Task succeeded: fastANI [2024-01-24 13:59:06,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:59:06,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:59:06,707] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:59:06,708] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:59:06,708] [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 dolosa strain=FDAARGOS_1463 GCA_019930785.1 152500 152500 type True 100.0 2061 2063 95 conclusive Burkholderia dolosa strain=LMG 18943 GCA_902499135.1 152500 152500 type True 99.943 1937 2063 95 conclusive Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 89.9373 1626 2063 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 89.9357 1627 2063 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 89.9219 1519 2063 95 below_threshold Burkholderia pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 89.909 1610 2063 95 below_threshold Burkholderia cenocepacia strain=NCTC13227 GCA_900446215.1 95486 95486 type True 89.8758 1632 2063 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 89.8632 1577 2063 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000959545.1 152480 152480 type True 89.7966 1656 2063 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000959525.1 87883 87883 type True 89.7925 1555 2063 95 below_threshold Burkholderia multivorans strain=NCTC13007 GCA_900446205.1 87883 87883 type True 89.7856 1577 2063 95 below_threshold Burkholderia seminalis strain=LMG 24067 GCA_902832885.1 488731 488731 type True 89.7464 1622 2063 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 89.7404 1667 2063 95 below_threshold Burkholderia anthina strain=LMG 20980 GCA_902830395.1 179879 179879 suspected-type True 89.6542 1592 2063 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000286555.1 87883 87883 type True 89.6438 1318 2063 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 89.6301 1585 2063 95 below_threshold Burkholderia anthina GCA_902498995.1 179879 179879 suspected-type True 89.6295 1578 2063 95 below_threshold Burkholderia seminalis GCA_902499165.1 488731 488731 type True 89.6083 1590 2063 95 below_threshold Burkholderia diffusa strain=DSM 23434 GCA_016836765.1 488732 488732 suspected-type True 89.4447 1585 2063 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 89.3216 1607 2063 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.4552 1467 2063 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.4495 1529 2063 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7159 1279 2063 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 82.067 1028 2063 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:59:06,709] [INFO] DFAST Taxonomy check result was written to GCF_019930785.1_ASM1993078v1_genomic.fna/tc_result.tsv [2024-01-24 13:59:06,710] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:59:06,710] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:59:06,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/checkm_data [2024-01-24 13:59:06,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:59:06,774] [INFO] Task started: CheckM [2024-01-24 13:59:06,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930785.1_ASM1993078v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930785.1_ASM1993078v1_genomic.fna/checkm_input GCF_019930785.1_ASM1993078v1_genomic.fna/checkm_result [2024-01-24 14:00:12,081] [INFO] Task succeeded: CheckM [2024-01-24 14:00:12,082] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:00:12,106] [INFO] ===== Completeness check finished ===== [2024-01-24 14:00:12,107] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:00:12,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930785.1_ASM1993078v1_genomic.fna/markers.fasta) [2024-01-24 14:00:12,108] [INFO] Task started: Blastn [2024-01-24 14:00:12,108] [INFO] Running command: blastn -query GCF_019930785.1_ASM1993078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47aa88f8-3dbc-423c-a8db-d05ea8210bbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930785.1_ASM1993078v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:00:14,433] [INFO] Task succeeded: Blastn [2024-01-24 14:00:14,437] [INFO] Selected 21 target genomes. [2024-01-24 14:00:14,437] [INFO] Target genome list was writen to GCF_019930785.1_ASM1993078v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:00:14,590] [INFO] Task started: fastANI [2024-01-24 14:00:14,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgce4e205e-7828-439a-b203-0ae90b82021b/GCF_019930785.1_ASM1993078v1_genomic.fna.gz --refList GCF_019930785.1_ASM1993078v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930785.1_ASM1993078v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:00:56,841] [INFO] Task succeeded: fastANI [2024-01-24 14:00:56,857] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:00:56,858] [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_902499135.1 s__Burkholderia dolosa 99.943 1937 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.52 98.66 0.97 0.91 15 conclusive GCF_000949135.2 s__Burkholderia sp000949135 90.0095 1595 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_902833145.1 s__Burkholderia sp902833145 89.936 1644 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_003853415.1 s__Burkholderia sp003853415 89.9162 1572 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_000292915.1 s__Burkholderia cepacia_D 89.9149 1488 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499075.1 s__Burkholderia pseudomultivorans 89.9101 1521 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_001028665.1 s__Burkholderia pyrrocinia 89.9022 1630 2063 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 89.8757 1622 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.44 95.03 0.88 0.83 18 - GCF_900446215.1 s__Burkholderia cenocepacia 89.8414 1636 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - GCF_001547525.1 s__Burkholderia anthina_A 89.8351 1698 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.44 98.20 0.94 0.91 13 - GCF_000959525.1 s__Burkholderia multivorans 89.7849 1556 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.58 96.90 0.90 0.85 326 - GCF_000203915.1 s__Burkholderia ambifaria 89.7666 1665 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.41 95.73 0.89 0.79 83 - GCF_902832885.1 s__Burkholderia seminalis 89.7521 1621 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.92 97.02 0.94 0.87 12 - GCF_003853645.1 s__Burkholderia sp003853645 89.7239 1551 2063 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 89.7033 1581 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_001742165.1 s__Burkholderia stabilis 89.7025 1611 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.17 98.56 0.94 0.88 6 - GCF_003853705.1 s__Burkholderia sp003853705 89.6684 1595 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001718315.1 s__Burkholderia diffusa_B 89.4009 1605 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.43 98.33 0.91 0.89 12 - GCF_001718835.1 s__Burkholderia cepacia_F 89.2937 1544 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000959245.1 s__Burkholderia ubonensis 88.6919 1513 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 - GCF_002097715.1 s__Burkholderia acidophila 88.451 1508 2063 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 - -------------------------------------------------------------------------------- [2024-01-24 14:00:56,859] [INFO] GTDB search result was written to GCF_019930785.1_ASM1993078v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:00:56,860] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:00:56,868] [INFO] DFAST_QC result json was written to GCF_019930785.1_ASM1993078v1_genomic.fna/dqc_result.json [2024-01-24 14:00:56,868] [INFO] DFAST_QC completed! [2024-01-24 14:00:56,869] [INFO] Total running time: 0h2m59s