[2024-01-24 13:25:28,177] [INFO] DFAST_QC pipeline started. [2024-01-24 13:25:28,179] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:25:28,180] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference [2024-01-24 13:25:29,451] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:25:29,452] [INFO] Task started: Prodigal [2024-01-24 13:25:29,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgbefcc4e6-44bd-4c29-af8b-a54ddce975a0/GCF_000759795.1_ASM75979v1_genomic.fna.gz | prodigal -d GCF_000759795.1_ASM75979v1_genomic.fna/cds.fna -a GCF_000759795.1_ASM75979v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:25:40,593] [INFO] Task succeeded: Prodigal [2024-01-24 13:25:40,593] [INFO] Task started: HMMsearch [2024-01-24 13:25:40,593] [INFO] Running command: hmmsearch --tblout GCF_000759795.1_ASM75979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/reference_markers.hmm GCF_000759795.1_ASM75979v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:25:40,901] [INFO] Task succeeded: HMMsearch [2024-01-24 13:25:40,902] [INFO] Found 6/6 markers. [2024-01-24 13:25:40,942] [INFO] Query marker FASTA was written to GCF_000759795.1_ASM75979v1_genomic.fna/markers.fasta [2024-01-24 13:25:40,942] [INFO] Task started: Blastn [2024-01-24 13:25:40,942] [INFO] Running command: blastn -query GCF_000759795.1_ASM75979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/reference_markers.fasta -out GCF_000759795.1_ASM75979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:25:41,836] [INFO] Task succeeded: Blastn [2024-01-24 13:25:41,840] [INFO] Selected 24 target genomes. [2024-01-24 13:25:41,841] [INFO] Target genome list was writen to GCF_000759795.1_ASM75979v1_genomic.fna/target_genomes.txt [2024-01-24 13:25:41,861] [INFO] Task started: fastANI [2024-01-24 13:25:41,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefcc4e6-44bd-4c29-af8b-a54ddce975a0/GCF_000759795.1_ASM75979v1_genomic.fna.gz --refList GCF_000759795.1_ASM75979v1_genomic.fna/target_genomes.txt --output GCF_000759795.1_ASM75979v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:26:06,103] [INFO] Task succeeded: fastANI [2024-01-24 13:26:06,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:26:06,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:26:06,128] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:26:06,128] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:26:06,129] [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 Pseudescherichia vulneris strain=NBRC 102420 GCA_000759795.1 566 566 type True 100.0 1424 1428 95 conclusive Pseudescherichia vulneris strain=NCTC12130 GCA_900450975.1 566 566 type True 99.9769 1427 1428 95 conclusive Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 82.2337 883 1428 95 below_threshold Enterobacter chengduensis strain=WCHECl-C4 = WCHECh050004 GCA_001984825.2 2494701 2494701 type True 82.2256 868 1428 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 82.1313 844 1428 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 81.9746 858 1428 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 81.9555 892 1428 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 81.8953 895 1428 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 81.8235 869 1428 95 below_threshold Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 81.7877 870 1428 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 81.6636 869 1428 95 below_threshold Klebsiella quasipneumoniae strain=DSM 28211 GCA_020115515.1 1463165 1463165 type True 81.4919 834 1428 95 below_threshold Klebsiella quasipneumoniae strain=FDAARGOS_1503 GCA_020099175.1 1463165 1463165 type True 81.4531 856 1428 95 below_threshold Klebsiella quasipneumoniae subsp. quasipneumoniae strain=01A030T GCA_020525925.1 1667327 1463165 type True 81.4398 847 1428 95 below_threshold Lelliottia nimipressuralis strain=CCUG 25894 GCA_004115925.1 69220 69220 type True 81.4296 859 1428 95 below_threshold Raoultella terrigena strain=NBRC 14941 GCA_006539725.1 577 577 type True 81.3515 829 1428 95 below_threshold Klebsiella pneumoniae strain=PartO-Kpneumoniae-RM8376 GCA_022869665.1 573 573 type True 81.3332 831 1428 95 below_threshold Klebsiella michiganensis strain=DSM 25444 GCA_002925905.1 1134687 1134687 type True 81.2523 800 1428 95 below_threshold Klebsiella michiganensis strain=CCUG 66515 GCA_009173485.1 1134687 1134687 type True 81.2459 805 1428 95 below_threshold Pseudocitrobacter corydidari GCA_021172065.1 2891570 2891570 type True 81.1572 787 1428 95 below_threshold Kluyvera sichuanensis strain=090646 GCA_014218705.1 2725494 2725494 type True 81.1371 814 1428 95 below_threshold Cronobacter universalis strain=NCTC 9529 GCA_000409325.1 535744 535744 type True 80.9817 803 1428 95 below_threshold Cronobacter universalis strain=NCTC 9529 GCA_900447325.1 535744 535744 type True 80.9525 812 1428 95 below_threshold Cronobacter universalis strain=NCTC 9529 GCA_000319325.1 535744 535744 type True 80.8396 813 1428 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:26:06,130] [INFO] DFAST Taxonomy check result was written to GCF_000759795.1_ASM75979v1_genomic.fna/tc_result.tsv [2024-01-24 13:26:06,131] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:26:06,131] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:26:06,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/checkm_data [2024-01-24 13:26:06,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:26:06,178] [INFO] Task started: CheckM [2024-01-24 13:26:06,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000759795.1_ASM75979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000759795.1_ASM75979v1_genomic.fna/checkm_input GCF_000759795.1_ASM75979v1_genomic.fna/checkm_result [2024-01-24 13:26:42,968] [INFO] Task succeeded: CheckM [2024-01-24 13:26:42,969] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:26:42,991] [INFO] ===== Completeness check finished ===== [2024-01-24 13:26:42,991] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:26:42,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000759795.1_ASM75979v1_genomic.fna/markers.fasta) [2024-01-24 13:26:42,992] [INFO] Task started: Blastn [2024-01-24 13:26:42,992] [INFO] Running command: blastn -query GCF_000759795.1_ASM75979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6ecb4cf-5ad7-4e8f-b8b8-d26baf844d20/dqc_reference/reference_markers_gtdb.fasta -out GCF_000759795.1_ASM75979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:26:44,202] [INFO] Task succeeded: Blastn [2024-01-24 13:26:44,207] [INFO] Selected 13 target genomes. [2024-01-24 13:26:44,207] [INFO] Target genome list was writen to GCF_000759795.1_ASM75979v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:26:44,224] [INFO] Task started: fastANI [2024-01-24 13:26:44,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefcc4e6-44bd-4c29-af8b-a54ddce975a0/GCF_000759795.1_ASM75979v1_genomic.fna.gz --refList GCF_000759795.1_ASM75979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000759795.1_ASM75979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:26:56,523] [INFO] Task succeeded: fastANI [2024-01-24 13:26:56,535] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:26:56,535] [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_000759795.1 s__Pseudescherichia vulneris 100.0 1424 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia 95.0 98.06 96.32 0.93 0.89 6 conclusive GCF_007680145.1 s__Pseudescherichia sp002298805 93.8733 1265 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia 95.0 98.55 96.56 0.95 0.92 13 - GCF_002918705.1 s__Pseudescherichia sp002918705 92.4162 1227 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia 95.0 98.58 97.76 0.93 0.92 5 - GCA_002480085.1 s__Pseudescherichia sp002480085 91.4058 1197 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia 95.0 N/A N/A N/A N/A 1 - GCF_001888805.2 s__Enterobacter_D sp001888805 82.7245 985 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D 95.0 97.70 97.19 0.94 0.94 3 - GCF_900116015.1 s__Enterobacter_D sp900116015 82.3328 943 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D 95.0 97.94 97.83 0.93 0.90 7 - GCF_004331265.1 s__Enterobacter wuhouensis 82.2395 882 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_019047785.1 s__Enterobacter cancerogenus 81.7839 871 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.78 98.42 0.93 0.90 16 - GCF_000751755.1 s__Klebsiella quasipneumoniae 81.5035 819 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 97.20 95.71 0.90 0.83 644 - GCF_006539725.1 s__Klebsiella terrigena 81.3515 829 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 97.25 96.63 0.88 0.85 68 - GCA_002377245.1 s__Phytobacter sp002377245 80.3138 661 1428 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:26:56,537] [INFO] GTDB search result was written to GCF_000759795.1_ASM75979v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:26:56,537] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:26:56,542] [INFO] DFAST_QC result json was written to GCF_000759795.1_ASM75979v1_genomic.fna/dqc_result.json [2024-01-24 13:26:56,542] [INFO] DFAST_QC completed! [2024-01-24 13:26:56,543] [INFO] Total running time: 0h1m28s