[2024-01-25 19:47:05,571] [INFO] DFAST_QC pipeline started. [2024-01-25 19:47:05,574] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:47:05,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference [2024-01-25 19:47:06,826] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:47:06,826] [INFO] Task started: Prodigal [2024-01-25 19:47:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a91d4f-f293-424d-89ff-ec2918dc3bc7/GCF_001457455.1_NCTC11397_genomic.fna.gz | prodigal -d GCF_001457455.1_NCTC11397_genomic.fna/cds.fna -a GCF_001457455.1_NCTC11397_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:47:14,089] [INFO] Task succeeded: Prodigal [2024-01-25 19:47:14,090] [INFO] Task started: HMMsearch [2024-01-25 19:47:14,090] [INFO] Running command: hmmsearch --tblout GCF_001457455.1_NCTC11397_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/reference_markers.hmm GCF_001457455.1_NCTC11397_genomic.fna/protein.faa > /dev/null [2024-01-25 19:47:14,279] [INFO] Task succeeded: HMMsearch [2024-01-25 19:47:14,280] [INFO] Found 6/6 markers. [2024-01-25 19:47:14,304] [INFO] Query marker FASTA was written to GCF_001457455.1_NCTC11397_genomic.fna/markers.fasta [2024-01-25 19:47:14,304] [INFO] Task started: Blastn [2024-01-25 19:47:14,304] [INFO] Running command: blastn -query GCF_001457455.1_NCTC11397_genomic.fna/markers.fasta -db /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/reference_markers.fasta -out GCF_001457455.1_NCTC11397_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:47:15,000] [INFO] Task succeeded: Blastn [2024-01-25 19:47:15,004] [INFO] Selected 5 target genomes. [2024-01-25 19:47:15,004] [INFO] Target genome list was writen to GCF_001457455.1_NCTC11397_genomic.fna/target_genomes.txt [2024-01-25 19:47:15,010] [INFO] Task started: fastANI [2024-01-25 19:47:15,010] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a91d4f-f293-424d-89ff-ec2918dc3bc7/GCF_001457455.1_NCTC11397_genomic.fna.gz --refList GCF_001457455.1_NCTC11397_genomic.fna/target_genomes.txt --output GCF_001457455.1_NCTC11397_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:47:18,552] [INFO] Task succeeded: fastANI [2024-01-25 19:47:18,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:47:18,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:47:18,558] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold) [2024-01-25 19:47:18,558] [INFO] The taxonomy check result is classified as 'inconclusive'. [2024-01-25 19:47:18,558] [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 Corynebacterium diphtheriae strain=NCTC11397 GCA_001457455.1 1717 1717 type True 100.0 818 821 95 inconclusive Corynebacterium diphtheriae GCA_902809765.1 1717 1717 type True 100.0 818 821 95 inconclusive Corynebacterium diphtheriae subsp. diphtheriae strain=FDAARGOS_1554 GCA_020736085.1 2315257 1717 type True 99.9998 817 821 95 inconclusive Corynebacterium diphtheriae strain=DSM 44123 GCA_001913265.1 1717 1717 type True 99.973 775 821 95 inconclusive Corynebacterium belfantii GCA_900205605.1 2014537 2014537 type True 95.083 692 821 95 inconclusive -------------------------------------------------------------------------------- [2024-01-25 19:47:18,560] [INFO] DFAST Taxonomy check result was written to GCF_001457455.1_NCTC11397_genomic.fna/tc_result.tsv [2024-01-25 19:47:18,560] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:47:18,560] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:47:18,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/checkm_data [2024-01-25 19:47:18,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:47:18,594] [INFO] Task started: CheckM [2024-01-25 19:47:18,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001457455.1_NCTC11397_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001457455.1_NCTC11397_genomic.fna/checkm_input GCF_001457455.1_NCTC11397_genomic.fna/checkm_result [2024-01-25 19:47:44,122] [INFO] Task succeeded: CheckM [2024-01-25 19:47:44,123] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 99.54% Contamintation: 1.56% Strain heterogeneity: 100.00% -------------------------------------------------------------------------------- [2024-01-25 19:47:44,144] [INFO] ===== Completeness check finished ===== [2024-01-25 19:47:44,144] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:47:44,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001457455.1_NCTC11397_genomic.fna/markers.fasta) [2024-01-25 19:47:44,145] [INFO] Task started: Blastn [2024-01-25 19:47:44,145] [INFO] Running command: blastn -query GCF_001457455.1_NCTC11397_genomic.fna/markers.fasta -db /var/lib/cwl/stg69506733-5d1b-46b9-9d26-a5dcb62a0787/dqc_reference/reference_markers_gtdb.fasta -out GCF_001457455.1_NCTC11397_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:47:45,112] [INFO] Task succeeded: Blastn [2024-01-25 19:47:45,114] [INFO] Selected 16 target genomes. [2024-01-25 19:47:45,114] [INFO] Target genome list was writen to GCF_001457455.1_NCTC11397_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:47:45,124] [INFO] Task started: fastANI [2024-01-25 19:47:45,124] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a91d4f-f293-424d-89ff-ec2918dc3bc7/GCF_001457455.1_NCTC11397_genomic.fna.gz --refList GCF_001457455.1_NCTC11397_genomic.fna/target_genomes_gtdb.txt --output GCF_001457455.1_NCTC11397_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:47:52,600] [INFO] Task succeeded: fastANI [2024-01-25 19:47:52,611] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:47:52,611] [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_001457455.1 s__Corynebacterium diphtheriae 100.0 817 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 98.05 95.03 0.92 0.83 346 conclusive GCF_902702935.1 s__Corynebacterium rouxii 92.7819 708 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_900187135.1 s__Corynebacterium ulcerans 80.2101 163 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 98.24 95.82 0.97 0.95 38 - GCF_001054945.1 s__Corynebacterium falsenii_A 80.1796 57 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_001941565.1 s__Corynebacterium phocae 79.5691 63 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 100.00 100.00 1.00 1.00 2 - GCF_002155265.1 s__Corynebacterium pseudotuberculosis 79.401 162 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 99.58 98.61 0.99 0.97 131 - GCF_000177535.2 s__Corynebacterium resistens 79.3116 66 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_000550805.1 s__Corynebacterium vitaeruminis 79.1731 143 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 98.86 98.60 0.94 0.94 3 - GCF_003814005.1 s__Corynebacterium pseudopelargi 79.1338 123 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_001020985.1 s__Corynebacterium mustelae 79.0582 90 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_004382825.2 s__Corynebacterium silvaticum 79.0203 169 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 99.94 99.78 1.00 0.99 8 - GCF_011612265.2 s__Corynebacterium matruchotii 78.992 70 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 98.54 97.18 0.97 0.91 9 - GCF_001767255.1 s__Corynebacterium sp001767255 78.8128 82 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 97.41 96.75 0.92 0.92 4 - GCF_004114895.1 s__Corynebacterium pelargi 78.7171 133 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 100.00 100.00 1.00 1.00 2 - GCF_014837045.1 s__Corynebacterium sp014837045 78.3794 93 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - GCF_003955685.1 s__Corynebacterium sp003955685 77.7818 86 821 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 19:47:52,612] [INFO] GTDB search result was written to GCF_001457455.1_NCTC11397_genomic.fna/result_gtdb.tsv [2024-01-25 19:47:52,613] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:47:52,615] [INFO] DFAST_QC result json was written to GCF_001457455.1_NCTC11397_genomic.fna/dqc_result.json [2024-01-25 19:47:52,615] [INFO] DFAST_QC completed! [2024-01-25 19:47:52,616] [INFO] Total running time: 0h0m47s