[2024-01-24 14:37:46,906] [INFO] DFAST_QC pipeline started. [2024-01-24 14:37:46,911] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:37:46,912] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference [2024-01-24 14:37:50,272] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:37:50,278] [INFO] Task started: Prodigal [2024-01-24 14:37:50,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbf1e249-0f01-4f8c-9880-3a3603a0818d/GCF_023721795.1_ASM2372179v1_genomic.fna.gz | prodigal -d GCF_023721795.1_ASM2372179v1_genomic.fna/cds.fna -a GCF_023721795.1_ASM2372179v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:38:01,452] [INFO] Task succeeded: Prodigal [2024-01-24 14:38:01,453] [INFO] Task started: HMMsearch [2024-01-24 14:38:01,453] [INFO] Running command: hmmsearch --tblout GCF_023721795.1_ASM2372179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/reference_markers.hmm GCF_023721795.1_ASM2372179v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:38:01,760] [INFO] Task succeeded: HMMsearch [2024-01-24 14:38:01,761] [INFO] Found 6/6 markers. [2024-01-24 14:38:01,801] [INFO] Query marker FASTA was written to GCF_023721795.1_ASM2372179v1_genomic.fna/markers.fasta [2024-01-24 14:38:01,802] [INFO] Task started: Blastn [2024-01-24 14:38:01,802] [INFO] Running command: blastn -query GCF_023721795.1_ASM2372179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/reference_markers.fasta -out GCF_023721795.1_ASM2372179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:38:02,854] [INFO] Task succeeded: Blastn [2024-01-24 14:38:02,857] [INFO] Selected 30 target genomes. [2024-01-24 14:38:02,857] [INFO] Target genome list was writen to GCF_023721795.1_ASM2372179v1_genomic.fna/target_genomes.txt [2024-01-24 14:38:02,878] [INFO] Task started: fastANI [2024-01-24 14:38:02,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbf1e249-0f01-4f8c-9880-3a3603a0818d/GCF_023721795.1_ASM2372179v1_genomic.fna.gz --refList GCF_023721795.1_ASM2372179v1_genomic.fna/target_genomes.txt --output GCF_023721795.1_ASM2372179v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:38:30,185] [INFO] Task succeeded: fastANI [2024-01-24 14:38:30,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:38:30,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:38:30,209] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold) [2024-01-24 14:38:30,210] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 14:38:30,210] [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 Schlegelella thermodepolymerans strain=DSM 15344 GCA_002933415.1 215580 215580 type True 78.9516 483 1285 95 below_threshold Schlegelella thermodepolymerans strain=DSM 15344 GCA_015476235.1 215580 215580 type True 78.8549 503 1285 95 below_threshold Ramlibacter algicola strain=CrO1 GCA_016641735.1 2795217 2795217 type True 78.1511 436 1285 95 below_threshold Sphaerotilus sulfidivorans strain=D-501 GCA_013426975.1 639200 639200 type True 78.1505 480 1285 95 below_threshold Cupriavidus alkaliphilus strain=ASC-732 GCA_900094595.1 942866 942866 type True 78.0997 481 1285 95 below_threshold Massilia agilis strain=JCM 31605 GCA_024756255.1 1811226 1811226 type True 78.0756 367 1285 95 below_threshold Sphaerotilus natans subsp. natans strain=DSM 6575 GCA_000689195.1 882627 34103 type True 78.0743 478 1285 95 below_threshold Sphaerotilus natans strain=ATCC 13338 GCA_900156335.1 34103 34103 type True 78.0702 496 1285 95 below_threshold Ralstonia solanacearum strain=K60 GCA_002251695.1 305 305 type True 78.0593 401 1285 95 below_threshold Massilia solisilvae strain=JCM 31607 GCA_024753215.1 1811225 1811225 type True 77.9936 381 1285 95 below_threshold Pigmentiphaga kullae strain=K24 GCA_004216695.1 151784 151784 type True 77.9537 387 1285 95 below_threshold Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 77.8742 341 1285 95 below_threshold Massilia horti strain=ONC3 GCA_004614195.1 2562153 2562153 type True 77.8463 326 1285 95 below_threshold Ramlibacter pinisoli strain=MAH-25 GCA_009758015.1 2682844 2682844 type True 77.7671 500 1285 95 below_threshold Bordetella pertussis strain=18323 GCA_000306945.1 520 520 type True 77.7615 355 1285 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 77.7339 467 1285 95 below_threshold Bordetella pertussis strain=FDAARGOS_1543 GCA_020736265.1 520 520 type True 77.6686 367 1285 95 below_threshold Massilia glaciei strain=B448-2 GCA_003011895.2 1524097 1524097 type True 77.6321 426 1285 95 below_threshold Castellaniella defragrans strain=DSM 12141 GCA_014203015.1 75697 75697 type True 77.6174 357 1285 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 77.5958 565 1285 95 below_threshold Bordetella parapertussis strain=FDAARGOS_1541 GCA_020735925.1 519 519 suspected-type True 77.5884 386 1285 95 below_threshold Massilia terrae strain=JCM 31606 GCA_024753145.1 1811224 1811224 type True 77.5783 398 1285 95 below_threshold Burkholderia gladioli strain=NBRC 13700 GCA_000739755.1 28095 28095 type True 77.5462 570 1285 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 77.5018 433 1285 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 77.4949 438 1285 95 below_threshold Bordetella bronchiseptica strain=CCUG 219 GCA_021391275.1 518 518 suspected-type True 77.4756 393 1285 95 below_threshold Verticiella sediminum strain=DSM 27279 GCA_007558815.1 1247510 1247510 type True 77.4456 386 1285 95 below_threshold Bordetella bronchiseptica strain=NBRC 13691 GCA_001598655.1 518 518 suspected-type True 77.3967 400 1285 95 below_threshold Bordetella bronchiseptica strain=NCTC452 GCA_900445725.1 518 518 suspected-type True 77.3941 422 1285 95 below_threshold Derxia lacustris strain=HL-12 GCA_002105195.1 764842 764842 type True 77.2722 443 1285 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:38:30,212] [INFO] DFAST Taxonomy check result was written to GCF_023721795.1_ASM2372179v1_genomic.fna/tc_result.tsv [2024-01-24 14:38:30,213] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:38:30,213] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:38:30,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/checkm_data [2024-01-24 14:38:30,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:38:30,260] [INFO] Task started: CheckM [2024-01-24 14:38:30,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023721795.1_ASM2372179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023721795.1_ASM2372179v1_genomic.fna/checkm_input GCF_023721795.1_ASM2372179v1_genomic.fna/checkm_result [2024-01-24 14:39:23,051] [INFO] Task succeeded: CheckM [2024-01-24 14:39:23,052] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:39:23,076] [INFO] ===== Completeness check finished ===== [2024-01-24 14:39:23,076] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:39:23,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023721795.1_ASM2372179v1_genomic.fna/markers.fasta) [2024-01-24 14:39:23,077] [INFO] Task started: Blastn [2024-01-24 14:39:23,077] [INFO] Running command: blastn -query GCF_023721795.1_ASM2372179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd96e4cc-792e-4af2-922c-aa876366df38/dqc_reference/reference_markers_gtdb.fasta -out GCF_023721795.1_ASM2372179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:39:24,905] [INFO] Task succeeded: Blastn [2024-01-24 14:39:24,910] [INFO] Selected 10 target genomes. [2024-01-24 14:39:24,910] [INFO] Target genome list was writen to GCF_023721795.1_ASM2372179v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:39:24,919] [INFO] Task started: fastANI [2024-01-24 14:39:24,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbf1e249-0f01-4f8c-9880-3a3603a0818d/GCF_023721795.1_ASM2372179v1_genomic.fna.gz --refList GCF_023721795.1_ASM2372179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023721795.1_ASM2372179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:39:36,836] [INFO] Task succeeded: fastANI [2024-01-24 14:39:36,854] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 14:39:36,855] [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 GCA_001724315.1 s__SCN-69-89 sp001724315 87.8701 598 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 N/A N/A N/A N/A 1 - GCF_008039575.1 s__SCN-69-89 sp008039575 87.3884 1003 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 N/A N/A N/A N/A 1 - GCA_012513825.1 s__SCN-69-89 sp012513825 82.4469 652 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 N/A N/A N/A N/A 1 - GCA_001724855.1 s__SCN-69-89 sp001724855 81.9986 653 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 N/A N/A N/A N/A 1 - GCA_003577305.1 s__SCN-69-89 sp003577305 81.5889 581 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 99.77 99.54 0.93 0.87 4 - GCA_001898645.1 s__SCN-69-89 sp001898645 81.4108 652 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 99.96 99.96 0.96 0.96 2 - GCF_014202215.1 s__Quisquiliibacterium transsilvanicum 80.5258 628 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Quisquiliibacterium 95.0 N/A N/A N/A N/A 1 - GCA_017307915.1 s__SCN-69-89 sp017307915 80.2001 538 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89 95.0 N/A N/A N/A N/A 1 - GCA_016710525.1 s__CAIZPE01 sp016710525 79.1068 553 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01 95.0 N/A N/A N/A N/A 1 - GCF_002188635.1 s__Pigmentiphaga sp002188635 77.843 392 1285 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga 95.0 99.65 99.31 0.97 0.93 3 - -------------------------------------------------------------------------------- [2024-01-24 14:39:36,856] [INFO] GTDB search result was written to GCF_023721795.1_ASM2372179v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:39:36,857] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:39:36,862] [INFO] DFAST_QC result json was written to GCF_023721795.1_ASM2372179v1_genomic.fna/dqc_result.json [2024-01-24 14:39:36,862] [INFO] DFAST_QC completed! [2024-01-24 14:39:36,862] [INFO] Total running time: 0h1m50s