[2024-01-24 15:02:33,556] [INFO] DFAST_QC pipeline started. [2024-01-24 15:02:33,558] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 15:02:33,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference [2024-01-24 15:02:34,823] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 15:02:34,824] [INFO] Task started: Prodigal [2024-01-24 15:02:34,824] [INFO] Running command: gunzip -c /var/lib/cwl/stge4a69294-ff1e-407f-968c-b2725b8d9f32/GCF_005860775.1_ASM586077v1_genomic.fna.gz | prodigal -d GCF_005860775.1_ASM586077v1_genomic.fna/cds.fna -a GCF_005860775.1_ASM586077v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 15:02:48,763] [INFO] Task succeeded: Prodigal [2024-01-24 15:02:48,764] [INFO] Task started: HMMsearch [2024-01-24 15:02:48,764] [INFO] Running command: hmmsearch --tblout GCF_005860775.1_ASM586077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/reference_markers.hmm GCF_005860775.1_ASM586077v1_genomic.fna/protein.faa > /dev/null [2024-01-24 15:02:49,090] [INFO] Task succeeded: HMMsearch [2024-01-24 15:02:49,092] [INFO] Found 6/6 markers. [2024-01-24 15:02:49,138] [INFO] Query marker FASTA was written to GCF_005860775.1_ASM586077v1_genomic.fna/markers.fasta [2024-01-24 15:02:49,139] [INFO] Task started: Blastn [2024-01-24 15:02:49,139] [INFO] Running command: blastn -query GCF_005860775.1_ASM586077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/reference_markers.fasta -out GCF_005860775.1_ASM586077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:02:50,174] [INFO] Task succeeded: Blastn [2024-01-24 15:02:50,178] [INFO] Selected 15 target genomes. [2024-01-24 15:02:50,179] [INFO] Target genome list was writen to GCF_005860775.1_ASM586077v1_genomic.fna/target_genomes.txt [2024-01-24 15:02:50,188] [INFO] Task started: fastANI [2024-01-24 15:02:50,188] [INFO] Running command: fastANI --query /var/lib/cwl/stge4a69294-ff1e-407f-968c-b2725b8d9f32/GCF_005860775.1_ASM586077v1_genomic.fna.gz --refList GCF_005860775.1_ASM586077v1_genomic.fna/target_genomes.txt --output GCF_005860775.1_ASM586077v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 15:03:10,106] [INFO] Task succeeded: fastANI [2024-01-24 15:03:10,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 15:03:10,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 15:03:10,121] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold) [2024-01-24 15:03:10,121] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 15:03:10,121] [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 indica strain=TOUT106 GCA_005860775.1 2582917 2582917 type True 100.0 1702 1704 95 conclusive Klebsiella michiganensis strain=DSM 25444 GCA_002925905.1 1134687 1134687 type True 86.5206 1262 1704 95 below_threshold Klebsiella michiganensis strain=CCUG 66515 GCA_009173485.1 1134687 1134687 type True 86.5027 1268 1704 95 below_threshold Klebsiella grimontii strain=06D021 GCA_900200035.1 2058152 2058152 type True 86.5006 1270 1704 95 below_threshold Klebsiella spallanzanii GCA_902158555.1 2587528 2587528 type True 86.4063 1279 1704 95 below_threshold Klebsiella pasteurii GCA_902158725.1 2587529 2587529 type True 86.294 1267 1704 95 below_threshold Klebsiella oxytoca strain=DSM 5175 GCA_020115535.1 571 571 type True 86.1287 1236 1704 95 below_threshold Klebsiella oxytoca strain=NCTC13727 GCA_900636985.1 571 571 type True 86.0895 1252 1704 95 below_threshold Klebsiella oxytoca strain=NBRC 105695 GCA_001598695.1 571 571 type True 86.0588 1244 1704 95 below_threshold Klebsiella huaxiensis strain=WCHKl090001 GCA_003261575.2 2153354 2153354 type True 86.0411 1261 1704 95 below_threshold Klebsiella pneumoniae strain=PartO-Kpneumoniae-RM8376 GCA_022869665.1 573 573 type True 82.7727 1055 1704 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 81.0281 768 1704 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 80.8664 781 1704 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 80.8083 765 1704 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 80.7348 793 1704 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 15:03:10,123] [INFO] DFAST Taxonomy check result was written to GCF_005860775.1_ASM586077v1_genomic.fna/tc_result.tsv [2024-01-24 15:03:10,124] [INFO] ===== Taxonomy check completed ===== [2024-01-24 15:03:10,124] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 15:03:10,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/checkm_data [2024-01-24 15:03:10,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 15:03:10,182] [INFO] Task started: CheckM [2024-01-24 15:03:10,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005860775.1_ASM586077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005860775.1_ASM586077v1_genomic.fna/checkm_input GCF_005860775.1_ASM586077v1_genomic.fna/checkm_result [2024-01-24 15:03:54,693] [INFO] Task succeeded: CheckM [2024-01-24 15:03:54,695] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 15:03:54,722] [INFO] ===== Completeness check finished ===== [2024-01-24 15:03:54,723] [INFO] ===== Start GTDB Search ===== [2024-01-24 15:03:54,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005860775.1_ASM586077v1_genomic.fna/markers.fasta) [2024-01-24 15:03:54,724] [INFO] Task started: Blastn [2024-01-24 15:03:54,724] [INFO] Running command: blastn -query GCF_005860775.1_ASM586077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4252abf5-c16d-4039-97f4-30eaedba5c4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_005860775.1_ASM586077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:03:56,188] [INFO] Task succeeded: Blastn [2024-01-24 15:03:56,191] [INFO] Selected 7 target genomes. [2024-01-24 15:03:56,191] [INFO] Target genome list was writen to GCF_005860775.1_ASM586077v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 15:03:56,197] [INFO] Task started: fastANI [2024-01-24 15:03:56,198] [INFO] Running command: fastANI --query /var/lib/cwl/stge4a69294-ff1e-407f-968c-b2725b8d9f32/GCF_005860775.1_ASM586077v1_genomic.fna.gz --refList GCF_005860775.1_ASM586077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005860775.1_ASM586077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 15:04:06,901] [INFO] Task succeeded: fastANI [2024-01-24 15:04:06,915] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 15:04:06,915] [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_005860775.1 s__Klebsiella indica 100.0 1702 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 99.34 99.34 0.92 0.92 2 conclusive GCF_002925905.1 s__Klebsiella michiganensis 86.5317 1261 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.53 97.41 0.90 0.83 291 - GCF_900200035.1 s__Klebsiella grimontii 86.5006 1270 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.56 95.68 0.89 0.83 175 - GCF_902158555.1 s__Klebsiella spallanzanii 86.419 1277 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 98.75 98.01 0.91 0.88 4 - GCF_001598695.1 s__Klebsiella oxytoca 86.0672 1242 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 99.31 98.97 0.94 0.89 181 - GCF_003261575.2 s__Klebsiella huaxiensis 86.0436 1261 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 96.95 95.21 0.89 0.84 9 - GCF_009707385.1 s__Klebsiella oxytoca_C 85.9333 1204 1704 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 15:04:06,917] [INFO] GTDB search result was written to GCF_005860775.1_ASM586077v1_genomic.fna/result_gtdb.tsv [2024-01-24 15:04:06,917] [INFO] ===== GTDB Search completed ===== [2024-01-24 15:04:06,923] [INFO] DFAST_QC result json was written to GCF_005860775.1_ASM586077v1_genomic.fna/dqc_result.json [2024-01-24 15:04:06,923] [INFO] DFAST_QC completed! [2024-01-24 15:04:06,923] [INFO] Total running time: 0h1m33s