[2024-01-25 17:36:35,415] [INFO] DFAST_QC pipeline started. [2024-01-25 17:36:35,416] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 17:36:35,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference [2024-01-25 17:36:36,551] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 17:36:36,552] [INFO] Task started: Prodigal [2024-01-25 17:36:36,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg74385766-2dc4-4076-b1e4-11165bc7168e/GCF_902859895.1_LMG_28138_genomic.fna.gz | prodigal -d GCF_902859895.1_LMG_28138_genomic.fna/cds.fna -a GCF_902859895.1_LMG_28138_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 17:36:54,524] [INFO] Task succeeded: Prodigal [2024-01-25 17:36:54,524] [INFO] Task started: HMMsearch [2024-01-25 17:36:54,524] [INFO] Running command: hmmsearch --tblout GCF_902859895.1_LMG_28138_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/reference_markers.hmm GCF_902859895.1_LMG_28138_genomic.fna/protein.faa > /dev/null [2024-01-25 17:36:54,799] [INFO] Task succeeded: HMMsearch [2024-01-25 17:36:54,800] [INFO] Found 6/6 markers. [2024-01-25 17:36:54,853] [INFO] Query marker FASTA was written to GCF_902859895.1_LMG_28138_genomic.fna/markers.fasta [2024-01-25 17:36:54,853] [INFO] Task started: Blastn [2024-01-25 17:36:54,853] [INFO] Running command: blastn -query GCF_902859895.1_LMG_28138_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/reference_markers.fasta -out GCF_902859895.1_LMG_28138_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 17:36:55,714] [INFO] Task succeeded: Blastn [2024-01-25 17:36:55,716] [INFO] Selected 33 target genomes. [2024-01-25 17:36:55,717] [INFO] Target genome list was writen to GCF_902859895.1_LMG_28138_genomic.fna/target_genomes.txt [2024-01-25 17:36:55,746] [INFO] Task started: fastANI [2024-01-25 17:36:55,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg74385766-2dc4-4076-b1e4-11165bc7168e/GCF_902859895.1_LMG_28138_genomic.fna.gz --refList GCF_902859895.1_LMG_28138_genomic.fna/target_genomes.txt --output GCF_902859895.1_LMG_28138_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 17:37:33,830] [INFO] Task succeeded: fastANI [2024-01-25 17:37:33,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 17:37:33,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 17:37:33,848] [INFO] Found 33 fastANI hits (1 hits with ANI > threshold) [2024-01-25 17:37:33,848] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 17:37:33,848] [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 Pararobbsia alpina strain=LMG 28138 GCA_902859895.1 621374 621374 type True 100.0 2123 2132 95 conclusive Burkholderia multivorans strain=NCTC13007 GCA_900446205.1 87883 87883 type True 79.4871 581 2132 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000286555.1 87883 87883 type True 79.4096 523 2132 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000959525.1 87883 87883 type True 79.3932 584 2132 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 79.3344 591 2132 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 79.3316 610 2132 95 below_threshold Burkholderia metallica GCA_902499065.1 488729 488729 type True 79.2957 573 2132 95 below_threshold Burkholderia stagnalis GCA_902499155.1 1503054 1503054 type True 79.1964 587 2132 95 below_threshold Burkholderia metallica strain=LMG 24068 GCA_902832845.1 488729 488729 type True 79.194 602 2132 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 79.1486 614 2132 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 79.1355 592 2132 95 below_threshold Burkholderia oklahomensis strain=LMG 23618 GCA_900608545.1 342113 342113 type True 79.0697 580 2132 95 below_threshold Paraburkholderia caballeronis strain=LMG 26416 GCA_900109675.1 416943 416943 type True 79.0581 650 2132 95 below_threshold Paraburkholderia flava strain=LD6 GCA_004359985.1 2547393 2547393 type True 79.0269 602 2132 95 below_threshold Burkholderia oklahomensis strain=C6786 GCA_000959365.1 342113 342113 type True 79.0175 579 2132 95 below_threshold Burkholderia oklahomensis strain=C6786 GCA_001522135.2 342113 342113 type True 79.0097 581 2132 95 below_threshold Paraburkholderia caballeronis strain=TNe-841 GCA_900104845.1 416943 416943 type True 79.009 654 2132 95 below_threshold Burkholderia thailandensis strain=E264 GCA_003568605.1 57975 57975 type True 78.9913 577 2132 95 below_threshold Burkholderia thailandensis strain=E264; ATCC 700388 GCA_000012365.1 57975 57975 type True 78.9833 580 2132 95 below_threshold Burkholderia oklahomensis strain=C6786 GCA_000170375.1 342113 342113 type True 78.9573 539 2132 95 below_threshold Burkholderia thailandensis strain=ATCC 700388 GCA_000152285.1 57975 57975 type True 78.92 539 2132 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 78.8524 694 2132 95 below_threshold Burkholderia pseudomallei strain=WRAIR 286 GCA_006538545.1 28450 28450 type True 78.8203 593 2132 95 below_threshold Burkholderia pseudomallei strain=ATCC 23343 GCA_001182285.1 28450 28450 type True 78.7595 616 2132 95 below_threshold Burkholderia gladioli strain=NBRC 13700 GCA_000739755.1 28095 28095 type True 78.7339 616 2132 95 below_threshold Burkholderia gladioli strain=NCTC12378 GCA_900446225.1 28095 28095 type True 78.7055 615 2132 95 below_threshold Paraburkholderia megapolitana strain=LMG 23650 GCA_900113825.1 420953 420953 type True 78.6511 556 2132 95 below_threshold Caballeronia ptereochthonis GCA_001545075.2 1777144 1777144 type True 78.6383 600 2132 95 below_threshold Paraburkholderia acidicola strain=ATCC 31363 GCA_002362315.1 1912599 1912599 type True 78.6351 542 2132 95 below_threshold Burkholderia gladioli strain=ATCC 10248 GCA_000959725.1 28095 28095 type True 78.6216 637 2132 95 below_threshold Paraburkholderia megapolitana strain=LMG 23650 GCA_007556815.1 420953 420953 type True 78.6112 560 2132 95 below_threshold Caballeronia cordobensis GCA_001544575.2 1353886 1353886 type True 78.4502 569 2132 95 below_threshold Caballeronia cordobensis strain=LMG 27620 GCA_001278535.1 1353886 1353886 type True 78.3667 579 2132 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 17:37:33,850] [INFO] DFAST Taxonomy check result was written to GCF_902859895.1_LMG_28138_genomic.fna/tc_result.tsv [2024-01-25 17:37:33,851] [INFO] ===== Taxonomy check completed ===== [2024-01-25 17:37:33,851] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 17:37:33,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/checkm_data [2024-01-25 17:37:33,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 17:37:33,914] [INFO] Task started: CheckM [2024-01-25 17:37:33,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859895.1_LMG_28138_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859895.1_LMG_28138_genomic.fna/checkm_input GCF_902859895.1_LMG_28138_genomic.fna/checkm_result [2024-01-25 17:38:27,375] [INFO] Task succeeded: CheckM [2024-01-25 17:38:27,376] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 17:38:27,398] [INFO] ===== Completeness check finished ===== [2024-01-25 17:38:27,398] [INFO] ===== Start GTDB Search ===== [2024-01-25 17:38:27,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859895.1_LMG_28138_genomic.fna/markers.fasta) [2024-01-25 17:38:27,399] [INFO] Task started: Blastn [2024-01-25 17:38:27,399] [INFO] Running command: blastn -query GCF_902859895.1_LMG_28138_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d84c06-2cab-4318-8094-98316f2c7789/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859895.1_LMG_28138_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 17:38:28,936] [INFO] Task succeeded: Blastn [2024-01-25 17:38:28,939] [INFO] Selected 26 target genomes. [2024-01-25 17:38:28,939] [INFO] Target genome list was writen to GCF_902859895.1_LMG_28138_genomic.fna/target_genomes_gtdb.txt [2024-01-25 17:38:28,954] [INFO] Task started: fastANI [2024-01-25 17:38:28,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg74385766-2dc4-4076-b1e4-11165bc7168e/GCF_902859895.1_LMG_28138_genomic.fna.gz --refList GCF_902859895.1_LMG_28138_genomic.fna/target_genomes_gtdb.txt --output GCF_902859895.1_LMG_28138_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 17:39:05,596] [INFO] Task succeeded: fastANI [2024-01-25 17:39:05,611] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 17:39:05,612] [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_902859895.1 s__Pararobbsia alpina 100.0 2123 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pararobbsia 95.0 N/A N/A N/A N/A 1 conclusive GCF_003628125.1 s__Pararobbsia silviterrae 80.9506 858 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pararobbsia 95.0 N/A N/A N/A N/A 1 - GCF_902499075.1 s__Burkholderia pseudomultivorans 79.3594 588 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_001718835.1 s__Burkholderia cepacia_F 79.3307 588 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000687455.2 s__Burkholderia sp000687455 79.2113 543 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001411805.1 s__Burkholderia plantarii 79.1266 599 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.45 95.52 0.94 0.88 5 - GCF_003635165.1 s__Burkholderia sp003635165 79.1101 612 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001931485.1 s__Paraburkholderia sp001931485 79.0767 616 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001524625.2 s__Burkholderia sp001524625 79.0658 570 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.38 99.33 0.93 0.91 11 - GCF_000959365.1 s__Burkholderia oklahomensis 79.0405 574 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.42 95.09 0.95 0.85 15 - GCF_900104845.1 s__Paraburkholderia caballeronis 79.0196 652 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.48 98.95 0.97 0.92 9 - GCF_902499045.1 s__Burkholderia latens 79.0185 590 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_902499135.1 s__Burkholderia dolosa 79.0154 579 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.52 98.66 0.97 0.91 15 - GCF_005280735.1 s__Trinickia sp005280735 78.981 636 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_000012365.1 s__Burkholderia thailandensis 78.9669 581 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.58 98.83 0.96 0.93 53 - GCF_003253405.1 s__Paraburkholderia sp003253405 78.8402 625 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003610295.1 s__Paraburkholderia sp003610295 78.7528 573 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001545075.1 s__Caballeronia ptereochthonis 78.659 597 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_002362315.1 s__Paraburkholderia acidophila 78.6349 542 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_007556815.1 s__Paraburkholderia megapolitana 78.6279 557 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.99 99.99 1.00 1.00 2 - GCF_000739775.1 s__Paraburkholderia heleia 78.6173 587 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.5542 N/A N/A N/A N/A 1 - GCF_000959725.1 s__Burkholderia gladioli 78.6173 636 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.34 97.08 0.90 0.82 265 - GCF_001522865.1 s__Burkholderia sp001522865 78.595 483 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003610895.1 s__Paraburkholderia fungorum_B 78.5732 564 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001718195.1 s__Paraburkholderia nodosa_A 78.5521 638 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001544575.2 s__Caballeronia cordobensis 78.4508 569 2132 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.18 97.54 0.94 0.91 5 - -------------------------------------------------------------------------------- [2024-01-25 17:39:05,613] [INFO] GTDB search result was written to GCF_902859895.1_LMG_28138_genomic.fna/result_gtdb.tsv [2024-01-25 17:39:05,614] [INFO] ===== GTDB Search completed ===== [2024-01-25 17:39:05,618] [INFO] DFAST_QC result json was written to GCF_902859895.1_LMG_28138_genomic.fna/dqc_result.json [2024-01-25 17:39:05,618] [INFO] DFAST_QC completed! [2024-01-25 17:39:05,618] [INFO] Total running time: 0h2m30s