[2024-01-24 12:25:20,317] [INFO] DFAST_QC pipeline started. [2024-01-24 12:25:20,320] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:25:20,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference [2024-01-24 12:25:21,576] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:25:21,577] [INFO] Task started: Prodigal [2024-01-24 12:25:21,577] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb731329-eb69-4fe9-86f6-55b0a76df848/GCF_024764775.1_ASM2476477v1_genomic.fna.gz | prodigal -d GCF_024764775.1_ASM2476477v1_genomic.fna/cds.fna -a GCF_024764775.1_ASM2476477v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:25:34,535] [INFO] Task succeeded: Prodigal [2024-01-24 12:25:34,536] [INFO] Task started: HMMsearch [2024-01-24 12:25:34,536] [INFO] Running command: hmmsearch --tblout GCF_024764775.1_ASM2476477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/reference_markers.hmm GCF_024764775.1_ASM2476477v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:25:34,832] [INFO] Task succeeded: HMMsearch [2024-01-24 12:25:34,834] [INFO] Found 6/6 markers. [2024-01-24 12:25:34,876] [INFO] Query marker FASTA was written to GCF_024764775.1_ASM2476477v1_genomic.fna/markers.fasta [2024-01-24 12:25:34,876] [INFO] Task started: Blastn [2024-01-24 12:25:34,876] [INFO] Running command: blastn -query GCF_024764775.1_ASM2476477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/reference_markers.fasta -out GCF_024764775.1_ASM2476477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:25:35,832] [INFO] Task succeeded: Blastn [2024-01-24 12:25:35,836] [INFO] Selected 27 target genomes. [2024-01-24 12:25:35,836] [INFO] Target genome list was writen to GCF_024764775.1_ASM2476477v1_genomic.fna/target_genomes.txt [2024-01-24 12:25:35,847] [INFO] Task started: fastANI [2024-01-24 12:25:35,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb731329-eb69-4fe9-86f6-55b0a76df848/GCF_024764775.1_ASM2476477v1_genomic.fna.gz --refList GCF_024764775.1_ASM2476477v1_genomic.fna/target_genomes.txt --output GCF_024764775.1_ASM2476477v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:26:02,098] [INFO] Task succeeded: fastANI [2024-01-24 12:26:02,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:26:02,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:26:02,124] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold) [2024-01-24 12:26:02,124] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 12:26:02,124] [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 Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 81.7502 881 1533 95 below_threshold Pseudocitrobacter corydidari GCA_021172065.1 2891570 2891570 type True 81.6922 916 1533 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 81.6876 906 1533 95 below_threshold Enterobacter chengduensis strain=WCHECl-C4 = WCHECh050004 GCA_001984825.2 2494701 2494701 type True 81.655 922 1533 95 below_threshold Kluyvera sichuanensis strain=090646 GCA_014218705.1 2725494 2725494 type True 81.6091 890 1533 95 below_threshold Enterobacter oligotrophicus strain=CCA6 GCA_009176645.1 2478464 2478464 type True 81.594 887 1533 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 81.5826 921 1533 95 below_threshold Kluyvera ascorbata strain=ATCC 33433 GCA_000735365.1 51288 51288 suspected-type True 81.5466 849 1533 95 below_threshold Enterobacter quasimori strain=090044 GCA_003964905.1 2838947 2838947 type True 81.5449 936 1533 95 below_threshold Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 81.5245 918 1533 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 81.5191 903 1533 95 below_threshold Kluyvera georgiana strain=ATCC 51603 GCA_001654985.1 73098 73098 type True 81.4849 850 1533 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 81.4355 885 1533 95 below_threshold Enterobacter hormaechei subsp. oharae strain=FDAARGOS_1533 GCA_020097195.1 301102 158836 type True 81.3731 931 1533 95 below_threshold Enterobacter mori strain=LMG 25706 GCA_000211415.1 539813 539813 type True 81.3631 895 1533 95 below_threshold Klebsiella quasivariicola strain=KPN1705 GCA_002269255.1 2026240 2026240 type True 81.2831 854 1533 95 below_threshold Pseudocitrobacter vendiensis strain=type strain: CPO20170097 GCA_943590815.1 2488306 2488306 type True 81.2302 887 1533 95 below_threshold Klebsiella variicola strain=DSM 15968 GCA_000828055.2 244366 244366 type True 81.2241 852 1533 95 below_threshold Raoultella terrigena strain=NBRC 14941 GCA_006539725.1 577 577 type True 81.1976 897 1533 95 below_threshold Kluyvera cryocrescens strain=NBRC 102467 GCA_001571285.1 580 580 type True 81.1248 882 1533 95 below_threshold Kluyvera intermedia strain=NCTC12125 GCA_900635475.1 61648 61648 suspected-type True 80.9443 820 1533 95 below_threshold Klebsiella spallanzanii GCA_902158555.1 2587528 2587528 type True 80.9181 846 1533 95 below_threshold Klebsiella pasteurii GCA_902158725.1 2587529 2587529 type True 80.8681 878 1533 95 below_threshold Klebsiella oxytoca strain=DSM 5175 GCA_020115535.1 571 571 type True 80.8394 836 1533 95 below_threshold Klebsiella oxytoca strain=NBRC 105695 GCA_001598695.1 571 571 type True 80.8121 843 1533 95 below_threshold Kluyvera intermedia strain=NBRC 102594 GCA_001598315.1 61648 61648 suspected-type True 80.8121 818 1533 95 below_threshold Citrobacter rodentium strain=DSM 16636 GCA_021278985.1 67825 67825 type True 80.702 824 1533 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:26:02,126] [INFO] DFAST Taxonomy check result was written to GCF_024764775.1_ASM2476477v1_genomic.fna/tc_result.tsv [2024-01-24 12:26:02,126] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:26:02,127] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:26:02,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/checkm_data [2024-01-24 12:26:02,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:26:02,170] [INFO] Task started: CheckM [2024-01-24 12:26:02,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024764775.1_ASM2476477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024764775.1_ASM2476477v1_genomic.fna/checkm_input GCF_024764775.1_ASM2476477v1_genomic.fna/checkm_result [2024-01-24 12:26:42,964] [INFO] Task succeeded: CheckM [2024-01-24 12:26:42,965] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:26:42,991] [INFO] ===== Completeness check finished ===== [2024-01-24 12:26:42,992] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:26:42,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024764775.1_ASM2476477v1_genomic.fna/markers.fasta) [2024-01-24 12:26:42,992] [INFO] Task started: Blastn [2024-01-24 12:26:42,993] [INFO] Running command: blastn -query GCF_024764775.1_ASM2476477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6cdb95-b9eb-49f8-8aab-0aff28a49a3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024764775.1_ASM2476477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:26:44,474] [INFO] Task succeeded: Blastn [2024-01-24 12:26:44,478] [INFO] Selected 8 target genomes. [2024-01-24 12:26:44,478] [INFO] Target genome list was writen to GCF_024764775.1_ASM2476477v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:26:44,487] [INFO] Task started: fastANI [2024-01-24 12:26:44,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb731329-eb69-4fe9-86f6-55b0a76df848/GCF_024764775.1_ASM2476477v1_genomic.fna.gz --refList GCF_024764775.1_ASM2476477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024764775.1_ASM2476477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:26:53,659] [INFO] Task succeeded: fastANI [2024-01-24 12:26:53,666] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:26:53,666] [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_902706235.1 s__Scandinavium sp902706235 99.4017 1473 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 conclusive GCA_902706205.1 s__Scandinavium sp902706205 93.9356 1348 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 - GCF_003935895.2 s__Scandinavium goeteborgense 93.2616 1271 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 97.59 96.23 0.90 0.88 4 - GCF_900215375.1 s__Scandinavium sp900215375 85.1707 1152 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 - GCA_002470465.1 s__Scandinavium sp002470465 84.8467 1113 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 - GCA_014156375.1 s__Scandinavium sp014156375 84.0719 1125 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 - GCA_009668205.1 s__Scandinavium sp009668205 83.7787 1103 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium 95.0 N/A N/A N/A N/A 1 - GCA_901456055.1 s__Phytobacter ursingii 80.5487 768 1533 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter 95.0 97.10 96.01 0.86 0.80 7 - -------------------------------------------------------------------------------- [2024-01-24 12:26:53,668] [INFO] GTDB search result was written to GCF_024764775.1_ASM2476477v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:26:53,669] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:26:53,677] [INFO] DFAST_QC result json was written to GCF_024764775.1_ASM2476477v1_genomic.fna/dqc_result.json [2024-01-24 12:26:53,677] [INFO] DFAST_QC completed! [2024-01-24 12:26:53,678] [INFO] Total running time: 0h1m33s