[2024-01-24 13:32:41,989] [INFO] DFAST_QC pipeline started. [2024-01-24 13:32:42,018] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:32:42,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference [2024-01-24 13:32:43,284] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:32:43,285] [INFO] Task started: Prodigal [2024-01-24 13:32:43,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg588aa056-0991-4198-965d-b4c89fafb2ef/GCF_001283065.1_Hheil_genomic.fna.gz | prodigal -d GCF_001283065.1_Hheil_genomic.fna/cds.fna -a GCF_001283065.1_Hheil_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:32:48,202] [INFO] Task succeeded: Prodigal [2024-01-24 13:32:48,202] [INFO] Task started: HMMsearch [2024-01-24 13:32:48,202] [INFO] Running command: hmmsearch --tblout GCF_001283065.1_Hheil_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/reference_markers.hmm GCF_001283065.1_Hheil_genomic.fna/protein.faa > /dev/null [2024-01-24 13:32:48,444] [INFO] Task succeeded: HMMsearch [2024-01-24 13:32:48,446] [INFO] Found 6/6 markers. [2024-01-24 13:32:48,468] [INFO] Query marker FASTA was written to GCF_001283065.1_Hheil_genomic.fna/markers.fasta [2024-01-24 13:32:48,468] [INFO] Task started: Blastn [2024-01-24 13:32:48,468] [INFO] Running command: blastn -query GCF_001283065.1_Hheil_genomic.fna/markers.fasta -db /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/reference_markers.fasta -out GCF_001283065.1_Hheil_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:32:49,052] [INFO] Task succeeded: Blastn [2024-01-24 13:32:49,057] [INFO] Selected 9 target genomes. [2024-01-24 13:32:49,058] [INFO] Target genome list was writen to GCF_001283065.1_Hheil_genomic.fna/target_genomes.txt [2024-01-24 13:32:49,069] [INFO] Task started: fastANI [2024-01-24 13:32:49,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg588aa056-0991-4198-965d-b4c89fafb2ef/GCF_001283065.1_Hheil_genomic.fna.gz --refList GCF_001283065.1_Hheil_genomic.fna/target_genomes.txt --output GCF_001283065.1_Hheil_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:32:52,418] [INFO] Task succeeded: fastANI [2024-01-24 13:32:52,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:32:52,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:32:52,434] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:32:52,434] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:32:52,434] [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 heilmannii GCA_001283065.1 35817 35817 type True 99.9998 543 544 95 conclusive Helicobacter heilmannii strain=LMG 26292 GCA_017979395.1 35817 35817 type True 99.8379 474 544 95 conclusive Helicobacter ailurogastricus GCA_001282945.1 1578720 1578720 type True 83.7436 424 544 95 below_threshold Helicobacter mehlei strain=L15 GCA_003660265.1 2316080 2316080 type True 78.6475 199 544 95 below_threshold Helicobacter vulpis strain=L2 GCA_003660395.1 2316076 2316076 type True 78.3095 159 544 95 below_threshold Helicobacter bizzozeronii strain=CIP 105233 GCA_017979515.1 56877 56877 type True 78.2413 200 544 95 below_threshold Helicobacter labacensis strain=L9 GCA_003660285.1 2316079 2316079 type True 77.8444 178 544 95 below_threshold Helicobacter suis strain=DSM 19735 GCA_017979375.1 104628 104628 type True 77.3494 99 544 95 below_threshold Helicobacter suis strain=HS1 GCA_000187625.2 104628 104628 type True 77.2971 100 544 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:32:52,436] [INFO] DFAST Taxonomy check result was written to GCF_001283065.1_Hheil_genomic.fna/tc_result.tsv [2024-01-24 13:32:52,437] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:32:52,438] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:32:52,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/checkm_data [2024-01-24 13:32:52,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:32:52,462] [INFO] Task started: CheckM [2024-01-24 13:32:52,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001283065.1_Hheil_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001283065.1_Hheil_genomic.fna/checkm_input GCF_001283065.1_Hheil_genomic.fna/checkm_result [2024-01-24 13:33:13,536] [INFO] Task succeeded: CheckM [2024-01-24 13:33:13,538] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 91.67% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:33:13,561] [INFO] ===== Completeness check finished ===== [2024-01-24 13:33:13,561] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:33:13,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001283065.1_Hheil_genomic.fna/markers.fasta) [2024-01-24 13:33:13,562] [INFO] Task started: Blastn [2024-01-24 13:33:13,563] [INFO] Running command: blastn -query GCF_001283065.1_Hheil_genomic.fna/markers.fasta -db /var/lib/cwl/stg313342ba-1418-46b6-9211-69de66273a1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001283065.1_Hheil_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:33:14,376] [INFO] Task succeeded: Blastn [2024-01-24 13:33:14,379] [INFO] Selected 12 target genomes. [2024-01-24 13:33:14,380] [INFO] Target genome list was writen to GCF_001283065.1_Hheil_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:33:14,396] [INFO] Task started: fastANI [2024-01-24 13:33:14,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg588aa056-0991-4198-965d-b4c89fafb2ef/GCF_001283065.1_Hheil_genomic.fna.gz --refList GCF_001283065.1_Hheil_genomic.fna/target_genomes_gtdb.txt --output GCF_001283065.1_Hheil_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:33:18,332] [INFO] Task succeeded: fastANI [2024-01-24 13:33:18,340] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:33:18,341] [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_001283065.1 s__Helicobacter_E heilmannii 99.9998 543 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.65 98.18 0.97 0.95 9 conclusive GCF_001282945.1 s__Helicobacter_E ailurogastricus 83.7654 423 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.41 98.32 0.95 0.92 6 - GCF_003660265.1 s__Helicobacter_E mehlei 78.6475 199 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 99.56 99.56 0.97 0.96 3 - GCA_000263275.1 s__Helicobacter_E bizzozeronii 78.4543 209 544 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_003660395.1 s__Helicobacter_E vulpis 78.3097 159 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 N/A N/A N/A N/A 1 - GCF_000200595.1 s__Helicobacter_E felis 78.2994 152 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 97.57 97.30 0.96 0.93 23 - GCF_003660285.1 s__Helicobacter_E labacensis 77.8631 177 544 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_902196125.1 s__Helicobacter_E suis_B 77.4071 107 544 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 96.42 96.42 0.94 0.90 3 - GCF_000187625.1 s__Helicobacter_E suis 77.2971 100 544 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 77.2969 99 544 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 13:33:18,342] [INFO] GTDB search result was written to GCF_001283065.1_Hheil_genomic.fna/result_gtdb.tsv [2024-01-24 13:33:18,343] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:33:18,346] [INFO] DFAST_QC result json was written to GCF_001283065.1_Hheil_genomic.fna/dqc_result.json [2024-01-24 13:33:18,346] [INFO] DFAST_QC completed! [2024-01-24 13:33:18,347] [INFO] Total running time: 0h0m36s