[2024-01-24 13:32:56,324] [INFO] DFAST_QC pipeline started. [2024-01-24 13:32:56,327] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:32:56,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference [2024-01-24 13:32:58,114] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:32:58,115] [INFO] Task started: Prodigal [2024-01-24 13:32:58,115] [INFO] Running command: gunzip -c /var/lib/cwl/stge4e85b8b-1922-4d7e-b491-14c0351a12cc/GCF_900625005.1_DSM_15824T_genomic.fna.gz | prodigal -d GCF_900625005.1_DSM_15824T_genomic.fna/cds.fna -a GCF_900625005.1_DSM_15824T_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:33:20,514] [INFO] Task succeeded: Prodigal [2024-01-24 13:33:20,515] [INFO] Task started: HMMsearch [2024-01-24 13:33:20,515] [INFO] Running command: hmmsearch --tblout GCF_900625005.1_DSM_15824T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/reference_markers.hmm GCF_900625005.1_DSM_15824T_genomic.fna/protein.faa > /dev/null [2024-01-24 13:33:20,818] [INFO] Task succeeded: HMMsearch [2024-01-24 13:33:20,819] [INFO] Found 6/6 markers. [2024-01-24 13:33:20,871] [INFO] Query marker FASTA was written to GCF_900625005.1_DSM_15824T_genomic.fna/markers.fasta [2024-01-24 13:33:20,871] [INFO] Task started: Blastn [2024-01-24 13:33:20,872] [INFO] Running command: blastn -query GCF_900625005.1_DSM_15824T_genomic.fna/markers.fasta -db /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/reference_markers.fasta -out GCF_900625005.1_DSM_15824T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:33:21,914] [INFO] Task succeeded: Blastn [2024-01-24 13:33:21,917] [INFO] Selected 10 target genomes. [2024-01-24 13:33:21,918] [INFO] Target genome list was writen to GCF_900625005.1_DSM_15824T_genomic.fna/target_genomes.txt [2024-01-24 13:33:21,921] [INFO] Task started: fastANI [2024-01-24 13:33:21,921] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e85b8b-1922-4d7e-b491-14c0351a12cc/GCF_900625005.1_DSM_15824T_genomic.fna.gz --refList GCF_900625005.1_DSM_15824T_genomic.fna/target_genomes.txt --output GCF_900625005.1_DSM_15824T_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:33:37,768] [INFO] Task succeeded: fastANI [2024-01-24 13:33:37,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:33:37,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:33:37,777] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold) [2024-01-24 13:33:37,777] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:33:37,777] [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 Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 100.0 2098 2098 95 conclusive Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 99.9934 2076 2098 95 conclusive Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 99.986 2074 2098 95 conclusive Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 94.315 1852 2098 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 94.286 1848 2098 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 91.1746 1796 2098 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 90.2996 1717 2098 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 89.1279 1675 2098 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.9996 1498 2098 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.2461 1332 2098 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:33:37,778] [INFO] DFAST Taxonomy check result was written to GCF_900625005.1_DSM_15824T_genomic.fna/tc_result.tsv [2024-01-24 13:33:37,779] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:33:37,779] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:33:37,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/checkm_data [2024-01-24 13:33:37,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:33:37,837] [INFO] Task started: CheckM [2024-01-24 13:33:37,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900625005.1_DSM_15824T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900625005.1_DSM_15824T_genomic.fna/checkm_input GCF_900625005.1_DSM_15824T_genomic.fna/checkm_result [2024-01-24 13:34:43,640] [INFO] Task succeeded: CheckM [2024-01-24 13:34:43,641] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:34:43,657] [INFO] ===== Completeness check finished ===== [2024-01-24 13:34:43,657] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:34:43,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900625005.1_DSM_15824T_genomic.fna/markers.fasta) [2024-01-24 13:34:43,657] [INFO] Task started: Blastn [2024-01-24 13:34:43,657] [INFO] Running command: blastn -query GCF_900625005.1_DSM_15824T_genomic.fna/markers.fasta -db /var/lib/cwl/stg0086af2b-6c73-42c2-935a-4aac151cd842/dqc_reference/reference_markers_gtdb.fasta -out GCF_900625005.1_DSM_15824T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:34:45,395] [INFO] Task succeeded: Blastn [2024-01-24 13:34:45,397] [INFO] Selected 14 target genomes. [2024-01-24 13:34:45,397] [INFO] Target genome list was writen to GCF_900625005.1_DSM_15824T_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:34:45,404] [INFO] Task started: fastANI [2024-01-24 13:34:45,404] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e85b8b-1922-4d7e-b491-14c0351a12cc/GCF_900625005.1_DSM_15824T_genomic.fna.gz --refList GCF_900625005.1_DSM_15824T_genomic.fna/target_genomes_gtdb.txt --output GCF_900625005.1_DSM_15824T_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:35:07,205] [INFO] Task succeeded: fastANI [2024-01-24 13:35:07,214] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:35:07,215] [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_001870465.1 s__Pseudomonas_E extremorientalis 99.986 2074 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.37 98.13 0.91 0.89 29 conclusive GCF_900103345.1 s__Pseudomonas_E azotoformans 94.3027 1868 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.97 95.87 0.94 0.87 9 - GCF_002007785.1 s__Pseudomonas_E azotoformans_B 91.1487 1816 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.95 98.86 0.94 0.92 6 - GCF_000612585.1 s__Pseudomonas_E sp000612585 90.8605 1666 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_001579805.1 s__Pseudomonas_E azotoformans_A 90.659 1757 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.75 96.24 0.87 0.84 8 - GCF_000503215.1 s__Pseudomonas_E canadensis 90.5769 1781 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.83 97.74 0.94 0.91 12 - GCF_013385825.1 s__Pseudomonas_E reactans 90.4917 1733 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.45 96.30 0.89 0.87 7 - GCF_001645105.1 s__Pseudomonas_E marginalis_B 90.3634 1696 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 - GCF_002563895.1 s__Pseudomonas_E lurida 90.2962 1718 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.19 99.03 0.94 0.91 25 - GCF_900111895.1 s__Pseudomonas_E simiae 90.215 1696 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.45 99.32 0.95 0.92 20 - GCF_001983175.1 s__Pseudomonas_E cedrina 89.164 1609 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 - GCF_012844475.1 s__Pseudomonas_E sp012844475 89.0658 1523 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCF_013386585.1 s__Pseudomonas_E sp013386585 89.005 1616 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_002837185.1 s__Pseudomonas_E fluorescens_AM 87.8204 1507 2098 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.23 99.16 0.96 0.94 7 - -------------------------------------------------------------------------------- [2024-01-24 13:35:07,216] [INFO] GTDB search result was written to GCF_900625005.1_DSM_15824T_genomic.fna/result_gtdb.tsv [2024-01-24 13:35:07,216] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:35:07,219] [INFO] DFAST_QC result json was written to GCF_900625005.1_DSM_15824T_genomic.fna/dqc_result.json [2024-01-24 13:35:07,219] [INFO] DFAST_QC completed! [2024-01-24 13:35:07,219] [INFO] Total running time: 0h2m11s