[2024-01-24 12:21:44,290] [INFO] DFAST_QC pipeline started. [2024-01-24 12:21:44,292] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:21:44,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference [2024-01-24 12:21:45,746] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:21:45,747] [INFO] Task started: Prodigal [2024-01-24 12:21:45,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg9825444d-bf18-45c0-bbbe-f81b9ad6914f/GCF_003261575.2_ASM326157v2_genomic.fna.gz | prodigal -d GCF_003261575.2_ASM326157v2_genomic.fna/cds.fna -a GCF_003261575.2_ASM326157v2_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:22:02,949] [INFO] Task succeeded: Prodigal [2024-01-24 12:22:02,949] [INFO] Task started: HMMsearch [2024-01-24 12:22:02,950] [INFO] Running command: hmmsearch --tblout GCF_003261575.2_ASM326157v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/reference_markers.hmm GCF_003261575.2_ASM326157v2_genomic.fna/protein.faa > /dev/null [2024-01-24 12:22:03,312] [INFO] Task succeeded: HMMsearch [2024-01-24 12:22:03,313] [INFO] Found 6/6 markers. [2024-01-24 12:22:03,363] [INFO] Query marker FASTA was written to GCF_003261575.2_ASM326157v2_genomic.fna/markers.fasta [2024-01-24 12:22:03,364] [INFO] Task started: Blastn [2024-01-24 12:22:03,364] [INFO] Running command: blastn -query GCF_003261575.2_ASM326157v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/reference_markers.fasta -out GCF_003261575.2_ASM326157v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:22:04,243] [INFO] Task succeeded: Blastn [2024-01-24 12:22:04,247] [INFO] Selected 14 target genomes. [2024-01-24 12:22:04,248] [INFO] Target genome list was writen to GCF_003261575.2_ASM326157v2_genomic.fna/target_genomes.txt [2024-01-24 12:22:04,255] [INFO] Task started: fastANI [2024-01-24 12:22:04,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg9825444d-bf18-45c0-bbbe-f81b9ad6914f/GCF_003261575.2_ASM326157v2_genomic.fna.gz --refList GCF_003261575.2_ASM326157v2_genomic.fna/target_genomes.txt --output GCF_003261575.2_ASM326157v2_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:22:24,006] [INFO] Task succeeded: fastANI [2024-01-24 12:22:24,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:22:24,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:22:24,019] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold) [2024-01-24 12:22:24,019] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:22:24,020] [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 Klebsiella huaxiensis strain=WCHKl090001 GCA_003261575.2 2153354 2153354 type True 100.0 2100 2100 95 conclusive Klebsiella spallanzanii GCA_902158555.1 2587528 2587528 type True 92.1319 1698 2100 95 below_threshold Klebsiella grimontii strain=06D021 GCA_900200035.1 2058152 2058152 type True 88.3665 1540 2100 95 below_threshold Klebsiella michiganensis strain=DSM 25444 GCA_002925905.1 1134687 1134687 type True 88.2705 1552 2100 95 below_threshold Klebsiella michiganensis strain=CCUG 66515 GCA_009173485.1 1134687 1134687 type True 88.1226 1536 2100 95 below_threshold Klebsiella pasteurii GCA_902158725.1 2587529 2587529 type True 88.0395 1533 2100 95 below_threshold Klebsiella oxytoca strain=NBRC 105695 GCA_001598695.1 571 571 type True 87.8145 1535 2100 95 below_threshold Klebsiella oxytoca strain=NCTC13727 GCA_900636985.1 571 571 type True 87.8006 1564 2100 95 below_threshold Klebsiella oxytoca strain=DSM 5175 GCA_020115535.1 571 571 type True 87.7846 1530 2100 95 below_threshold Klebsiella pneumoniae strain=PartO-Kpneumoniae-RM8376 GCA_022869665.1 573 573 type True 83.4897 1240 2100 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 81.6214 856 2100 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 81.3372 878 2100 95 below_threshold Citrobacter rodentium strain=DSM 16636 GCA_021278985.1 67825 67825 type True 81.237 911 2100 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 81.2365 878 2100 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:22:24,021] [INFO] DFAST Taxonomy check result was written to GCF_003261575.2_ASM326157v2_genomic.fna/tc_result.tsv [2024-01-24 12:22:24,022] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:22:24,022] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:22:24,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/checkm_data [2024-01-24 12:22:24,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:22:24,082] [INFO] Task started: CheckM [2024-01-24 12:22:24,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003261575.2_ASM326157v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003261575.2_ASM326157v2_genomic.fna/checkm_input GCF_003261575.2_ASM326157v2_genomic.fna/checkm_result [2024-01-24 12:23:15,165] [INFO] Task succeeded: CheckM [2024-01-24 12:23:15,167] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:23:15,197] [INFO] ===== Completeness check finished ===== [2024-01-24 12:23:15,198] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:23:15,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003261575.2_ASM326157v2_genomic.fna/markers.fasta) [2024-01-24 12:23:15,198] [INFO] Task started: Blastn [2024-01-24 12:23:15,199] [INFO] Running command: blastn -query GCF_003261575.2_ASM326157v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa69e0a-cafd-4079-9d25-272070d28d22/dqc_reference/reference_markers_gtdb.fasta -out GCF_003261575.2_ASM326157v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:23:16,394] [INFO] Task succeeded: Blastn [2024-01-24 12:23:16,398] [INFO] Selected 11 target genomes. [2024-01-24 12:23:16,398] [INFO] Target genome list was writen to GCF_003261575.2_ASM326157v2_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:23:16,406] [INFO] Task started: fastANI [2024-01-24 12:23:16,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg9825444d-bf18-45c0-bbbe-f81b9ad6914f/GCF_003261575.2_ASM326157v2_genomic.fna.gz --refList GCF_003261575.2_ASM326157v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003261575.2_ASM326157v2_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:23:32,343] [INFO] Task succeeded: fastANI [2024-01-24 12:23:32,353] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:23:32,353] [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_003261575.2 s__Klebsiella huaxiensis 100.0 2100 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 96.95 95.21 0.89 0.84 9 conclusive GCF_902158555.1 s__Klebsiella spallanzanii 92.1319 1698 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.75 98.01 0.91 0.88 4 - GCF_900200035.1 s__Klebsiella grimontii 88.3719 1540 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.56 95.68 0.89 0.83 175 - GCF_002925905.1 s__Klebsiella michiganensis 88.262 1554 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.53 97.41 0.90 0.83 291 - GCF_001598695.1 s__Klebsiella oxytoca 87.8116 1536 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 99.31 98.97 0.94 0.89 181 - GCF_009707385.1 s__Klebsiella oxytoca_C 87.6321 1462 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 N/A N/A N/A N/A 1 - GCF_005860775.1 s__Klebsiella indica 85.8239 1281 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 99.34 99.34 0.92 0.92 2 - GCF_004342285.1 s__Klebsiella sp004342285 84.1396 1244 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 N/A N/A N/A N/A 1 - GCF_002208095.1 s__Enterobacter cloacae_M 81.5802 934 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.7528 98.28 96.89 0.91 0.85 84 - GCF_001729765.1 s__Enterobacter kobei 81.5348 880 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.81 98.45 0.89 0.85 141 - GCF_013337685.1 s__Citrobacter gillenii 81.3067 835 2100 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter 95.0 98.72 97.36 0.89 0.84 39 - -------------------------------------------------------------------------------- [2024-01-24 12:23:32,356] [INFO] GTDB search result was written to GCF_003261575.2_ASM326157v2_genomic.fna/result_gtdb.tsv [2024-01-24 12:23:32,361] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:23:32,365] [INFO] DFAST_QC result json was written to GCF_003261575.2_ASM326157v2_genomic.fna/dqc_result.json [2024-01-24 12:23:32,365] [INFO] DFAST_QC completed! [2024-01-24 12:23:32,365] [INFO] Total running time: 0h1m48s