[2024-01-24 12:23:04,034] [INFO] DFAST_QC pipeline started. [2024-01-24 12:23:04,035] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:23:04,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference [2024-01-24 12:23:05,442] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:23:05,443] [INFO] Task started: Prodigal [2024-01-24 12:23:05,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg08dcb896-69c3-41f5-8edf-8d4ec5b1191f/GCF_025998115.1_ASM2599811v1_genomic.fna.gz | prodigal -d GCF_025998115.1_ASM2599811v1_genomic.fna/cds.fna -a GCF_025998115.1_ASM2599811v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:23:10,282] [INFO] Task succeeded: Prodigal [2024-01-24 12:23:10,283] [INFO] Task started: HMMsearch [2024-01-24 12:23:10,283] [INFO] Running command: hmmsearch --tblout GCF_025998115.1_ASM2599811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/reference_markers.hmm GCF_025998115.1_ASM2599811v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:23:10,518] [INFO] Task succeeded: HMMsearch [2024-01-24 12:23:10,520] [INFO] Found 6/6 markers. [2024-01-24 12:23:10,544] [INFO] Query marker FASTA was written to GCF_025998115.1_ASM2599811v1_genomic.fna/markers.fasta [2024-01-24 12:23:10,544] [INFO] Task started: Blastn [2024-01-24 12:23:10,544] [INFO] Running command: blastn -query GCF_025998115.1_ASM2599811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/reference_markers.fasta -out GCF_025998115.1_ASM2599811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:23:11,123] [INFO] Task succeeded: Blastn [2024-01-24 12:23:11,126] [INFO] Selected 8 target genomes. [2024-01-24 12:23:11,127] [INFO] Target genome list was writen to GCF_025998115.1_ASM2599811v1_genomic.fna/target_genomes.txt [2024-01-24 12:23:11,132] [INFO] Task started: fastANI [2024-01-24 12:23:11,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg08dcb896-69c3-41f5-8edf-8d4ec5b1191f/GCF_025998115.1_ASM2599811v1_genomic.fna.gz --refList GCF_025998115.1_ASM2599811v1_genomic.fna/target_genomes.txt --output GCF_025998115.1_ASM2599811v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:23:13,817] [INFO] Task succeeded: fastANI [2024-01-24 12:23:13,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:23:13,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:23:13,830] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold) [2024-01-24 12:23:13,831] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:23:13,831] [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 Helicobacter ailurogastricus GCA_001282945.1 1578720 1578720 type True 99.893 517 534 95 conclusive Helicobacter heilmannii strain=LMG 26292 GCA_017979395.1 35817 35817 type True 83.7304 379 534 95 below_threshold Helicobacter heilmannii GCA_001283065.1 35817 35817 type True 83.6305 411 534 95 below_threshold Helicobacter mehlei strain=L15 GCA_003660265.1 2316080 2316080 type True 79.1601 214 534 95 below_threshold Helicobacter bizzozeronii strain=CIP 105233 GCA_017979515.1 56877 56877 type True 78.7922 237 534 95 below_threshold Helicobacter suis strain=HS1 GCA_000187625.2 104628 104628 type True 77.3742 134 534 95 below_threshold Helicobacter suis strain=DSM 19735 GCA_017979375.1 104628 104628 type True 77.1864 133 534 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:23:13,832] [INFO] DFAST Taxonomy check result was written to GCF_025998115.1_ASM2599811v1_genomic.fna/tc_result.tsv [2024-01-24 12:23:13,833] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:23:13,833] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:23:13,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/checkm_data [2024-01-24 12:23:13,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:23:13,859] [INFO] Task started: CheckM [2024-01-24 12:23:13,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025998115.1_ASM2599811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025998115.1_ASM2599811v1_genomic.fna/checkm_input GCF_025998115.1_ASM2599811v1_genomic.fna/checkm_result [2024-01-24 12:23:34,149] [INFO] Task succeeded: CheckM [2024-01-24 12:23:34,150] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 91.67% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:23:34,174] [INFO] ===== Completeness check finished ===== [2024-01-24 12:23:34,174] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:23:34,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025998115.1_ASM2599811v1_genomic.fna/markers.fasta) [2024-01-24 12:23:34,175] [INFO] Task started: Blastn [2024-01-24 12:23:34,175] [INFO] Running command: blastn -query GCF_025998115.1_ASM2599811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9402f71-a3ba-4f8d-b582-a1d1730b6a17/dqc_reference/reference_markers_gtdb.fasta -out GCF_025998115.1_ASM2599811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:23:34,933] [INFO] Task succeeded: Blastn [2024-01-24 12:23:34,938] [INFO] Selected 12 target genomes. [2024-01-24 12:23:34,938] [INFO] Target genome list was writen to GCF_025998115.1_ASM2599811v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:23:34,948] [INFO] Task started: fastANI [2024-01-24 12:23:34,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg08dcb896-69c3-41f5-8edf-8d4ec5b1191f/GCF_025998115.1_ASM2599811v1_genomic.fna.gz --refList GCF_025998115.1_ASM2599811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025998115.1_ASM2599811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:23:38,947] [INFO] Task succeeded: fastANI [2024-01-24 12:23:38,961] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:23:38,962] [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_001282945.1 s__Helicobacter_E ailurogastricus 99.893 517 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.41 98.32 0.95 0.92 6 conclusive GCF_001283065.1 s__Helicobacter_E heilmannii 83.603 412 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.65 98.18 0.97 0.95 9 - GCF_003660265.1 s__Helicobacter_E mehlei 79.1601 214 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 99.56 99.56 0.97 0.96 3 - GCF_000200595.1 s__Helicobacter_E felis 78.8014 191 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 97.57 97.30 0.96 0.93 23 - GCA_000263275.1 s__Helicobacter_E bizzozeronii 78.7965 251 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 96.96 95.19 0.90 0.83 11 - GCF_003660285.1 s__Helicobacter_E labacensis 78.1821 206 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.30 98.30 0.89 0.89 2 - GCF_000187625.1 s__Helicobacter_E suis 77.3931 133 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 99.74 99.56 0.96 0.89 27 - GCF_902196135.1 s__Helicobacter_E suis_A 77.2143 132 534 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 97.68 97.34 0.95 0.91 4 - -------------------------------------------------------------------------------- [2024-01-24 12:23:38,965] [INFO] GTDB search result was written to GCF_025998115.1_ASM2599811v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:23:38,966] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:23:38,969] [INFO] DFAST_QC result json was written to GCF_025998115.1_ASM2599811v1_genomic.fna/dqc_result.json [2024-01-24 12:23:38,969] [INFO] DFAST_QC completed! [2024-01-24 12:23:38,970] [INFO] Total running time: 0h0m35s