[2024-01-24 12:22:34,052] [INFO] DFAST_QC pipeline started. [2024-01-24 12:22:34,062] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:22:34,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference [2024-01-24 12:22:35,712] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:22:35,712] [INFO] Task started: Prodigal [2024-01-24 12:22:35,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg21d39c98-c920-45a6-ac01-da254d37fa5d/GCF_018987305.1_ASM1898730v1_genomic.fna.gz | prodigal -d GCF_018987305.1_ASM1898730v1_genomic.fna/cds.fna -a GCF_018987305.1_ASM1898730v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:22:46,516] [INFO] Task succeeded: Prodigal [2024-01-24 12:22:46,516] [INFO] Task started: HMMsearch [2024-01-24 12:22:46,516] [INFO] Running command: hmmsearch --tblout GCF_018987305.1_ASM1898730v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/reference_markers.hmm GCF_018987305.1_ASM1898730v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:22:46,746] [INFO] Task succeeded: HMMsearch [2024-01-24 12:22:46,748] [INFO] Found 6/6 markers. [2024-01-24 12:22:46,784] [INFO] Query marker FASTA was written to GCF_018987305.1_ASM1898730v1_genomic.fna/markers.fasta [2024-01-24 12:22:46,784] [INFO] Task started: Blastn [2024-01-24 12:22:46,785] [INFO] Running command: blastn -query GCF_018987305.1_ASM1898730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/reference_markers.fasta -out GCF_018987305.1_ASM1898730v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:22:47,563] [INFO] Task succeeded: Blastn [2024-01-24 12:22:47,565] [INFO] Selected 17 target genomes. [2024-01-24 12:22:47,565] [INFO] Target genome list was writen to GCF_018987305.1_ASM1898730v1_genomic.fna/target_genomes.txt [2024-01-24 12:22:47,579] [INFO] Task started: fastANI [2024-01-24 12:22:47,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d39c98-c920-45a6-ac01-da254d37fa5d/GCF_018987305.1_ASM1898730v1_genomic.fna.gz --refList GCF_018987305.1_ASM1898730v1_genomic.fna/target_genomes.txt --output GCF_018987305.1_ASM1898730v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:23:05,416] [INFO] Task succeeded: fastANI [2024-01-24 12:23:05,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:23:05,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:23:05,427] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold) [2024-01-24 12:23:05,427] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:23:05,427] [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 Leclercia pneumoniae strain=49125 GCA_018987305.1 2815358 2815358 type True 100.0 1464 1464 95 conclusive Leclercia pneumoniae strain=49125 GCA_017348915.1 2815358 2815358 type True 99.9961 1461 1464 95 conclusive Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 84.6943 1072 1464 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 84.5166 1051 1464 95 below_threshold Leclercia adecarboxylata strain=FDAARGOS_1505 GCA_020097395.1 83655 83655 suspected-type True 84.4316 1138 1464 95 below_threshold Enterobacter hormaechei subsp. hormaechei strain=ATCC 49162 GCA_001875655.1 301105 158836 type True 84.3293 1052 1464 95 below_threshold Enterobacter oligotrophicus strain=CCA6 GCA_009176645.1 2478464 2478464 type True 84.3072 1067 1464 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 84.3057 1069 1464 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 84.2913 1059 1464 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 84.2436 1020 1464 95 below_threshold Enterobacter hormaechei subsp. hoffmannii strain=DSM 14563 GCA_001729745.1 1812934 158836 type True 84.2231 1050 1464 95 below_threshold Leclercia adecarboxylata strain=ATCC 23216 GCA_000735515.1 83655 83655 suspected-type True 84.2177 1107 1464 95 below_threshold Leclercia adecarboxylata strain=NBRC 102595 GCA_001515505.1 83655 83655 suspected-type True 84.1994 1127 1464 95 below_threshold Enterobacter hormaechei subsp. hormaechei strain=ATCC 49162 GCA_000213995.1 301105 158836 type True 84.1969 1047 1464 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 84.186 1081 1464 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 84.0024 1057 1464 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 83.9443 1035 1464 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:23:05,429] [INFO] DFAST Taxonomy check result was written to GCF_018987305.1_ASM1898730v1_genomic.fna/tc_result.tsv [2024-01-24 12:23:05,429] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:23:05,429] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:23:05,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/checkm_data [2024-01-24 12:23:05,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:23:05,473] [INFO] Task started: CheckM [2024-01-24 12:23:05,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018987305.1_ASM1898730v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018987305.1_ASM1898730v1_genomic.fna/checkm_input GCF_018987305.1_ASM1898730v1_genomic.fna/checkm_result [2024-01-24 12:23:39,843] [INFO] Task succeeded: CheckM [2024-01-24 12:23:39,844] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:23:39,859] [INFO] ===== Completeness check finished ===== [2024-01-24 12:23:39,859] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:23:39,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018987305.1_ASM1898730v1_genomic.fna/markers.fasta) [2024-01-24 12:23:39,860] [INFO] Task started: Blastn [2024-01-24 12:23:39,860] [INFO] Running command: blastn -query GCF_018987305.1_ASM1898730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd27ab2-c9d3-4b88-854f-9a9c31fd719a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018987305.1_ASM1898730v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:23:41,040] [INFO] Task succeeded: Blastn [2024-01-24 12:23:41,043] [INFO] Selected 23 target genomes. [2024-01-24 12:23:41,043] [INFO] Target genome list was writen to GCF_018987305.1_ASM1898730v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:23:41,054] [INFO] Task started: fastANI [2024-01-24 12:23:41,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d39c98-c920-45a6-ac01-da254d37fa5d/GCF_018987305.1_ASM1898730v1_genomic.fna.gz --refList GCF_018987305.1_ASM1898730v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018987305.1_ASM1898730v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:24:06,061] [INFO] Task succeeded: fastANI [2024-01-24 12:24:06,075] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:24:06,075] [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_017348915.1 s__UBA7405 sp000755535 99.9955 1462 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405 95.0 98.56 97.85 0.93 0.89 10 conclusive GCA_002469605.1 s__UBA7405 sp002469605 85.3881 796 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405 95.0 N/A N/A N/A N/A 1 - GCF_019047785.1 s__Enterobacter cancerogenus 84.6984 1071 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.78 98.42 0.93 0.90 16 - GCF_006874705.1 s__Leclercia adecarboxylata_C 84.6676 1138 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.71 98.25 0.93 0.90 13 - GCF_006171285.1 s__Leclercia adecarboxylata_A 84.6391 1165 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 97.80 96.55 0.92 0.89 4 - GCA_002360945.1 s__Leclercia adecarboxylata_B 84.4426 1114 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 99.97 99.97 0.98 0.98 2 - GCF_009176645.1 s__Enterobacter oligotrophicus 84.3205 1065 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.55 99.09 0.97 0.94 3 - GCF_003594935.1 s__Enterobacter huaxiensis 84.3041 1070 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.98 98.98 0.94 0.94 2 - GCF_900324475.1 s__Enterobacter bugandensis 84.3032 1067 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.49 95.52 0.94 0.88 115 - GCA_901472455.1 s__Leclercia adecarboxylata 84.2671 1121 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.53 98.09 0.95 0.87 86 - GCF_011754535.1 s__Enterobacter cloacae_N 84.2335 1062 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.03 98.99 0.93 0.91 4 - GCF_003594915.1 s__Enterobacter chuandaensis 84.2331 1029 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 98.32 0.92 0.92 3 - GCF_001729745.1 s__Enterobacter hormaechei_A 84.2143 1052 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 96.63 95.22 0.89 0.83 1867 - GCF_008364625.1 s__Enterobacter dykesii 84.2012 1020 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.5795 99.13 97.97 0.97 0.95 7 - GCF_009755685.1 s__Enterobacter sp000568095 84.1975 1065 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0476 98.37 98.04 0.95 0.92 11 - GCF_004331265.1 s__Enterobacter wuhouensis 84.1948 1080 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_007035645.1 s__Enterobacter asburiae_B 84.1831 1076 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.31 97.34 0.92 0.85 70 - GCF_000025565.1 s__Enterobacter cloacae 84.1791 1074 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.05 95.14 0.91 0.80 129 - GCF_000211415.1 s__Enterobacter mori 84.1023 1043 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.59 96.13 0.88 0.85 23 - GCF_003057745.1 s__Enterobacter sp003057745 83.8611 994 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_009363175.1 s__Citrobacter_A telavivensis 81.7646 841 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A 95.0 99.99 99.99 1.00 1.00 2 - GCF_004353845.1 s__Citrobacter freundii_E 81.4066 801 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter 95.0 99.27 99.27 0.92 0.92 2 - GCF_010231475.1 s__Citrobacter sp010231475 81.0343 752 1464 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:24:06,077] [INFO] GTDB search result was written to GCF_018987305.1_ASM1898730v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:24:06,077] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:24:06,081] [INFO] DFAST_QC result json was written to GCF_018987305.1_ASM1898730v1_genomic.fna/dqc_result.json [2024-01-24 12:24:06,081] [INFO] DFAST_QC completed! [2024-01-24 12:24:06,081] [INFO] Total running time: 0h1m32s