[2024-01-24 12:25:20,630] [INFO] DFAST_QC pipeline started. [2024-01-24 12:25:20,632] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:25:20,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference [2024-01-24 12:25:21,875] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:25:21,876] [INFO] Task started: Prodigal [2024-01-24 12:25:21,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg26f9ab82-5a67-46ef-9c92-18c270d699cc/GCF_016836765.1_ASM1683676v1_genomic.fna.gz | prodigal -d GCF_016836765.1_ASM1683676v1_genomic.fna/cds.fna -a GCF_016836765.1_ASM1683676v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:25:42,919] [INFO] Task succeeded: Prodigal [2024-01-24 12:25:42,920] [INFO] Task started: HMMsearch [2024-01-24 12:25:42,920] [INFO] Running command: hmmsearch --tblout GCF_016836765.1_ASM1683676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/reference_markers.hmm GCF_016836765.1_ASM1683676v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:25:43,258] [INFO] Task succeeded: HMMsearch [2024-01-24 12:25:43,260] [INFO] Found 6/6 markers. [2024-01-24 12:25:43,323] [INFO] Query marker FASTA was written to GCF_016836765.1_ASM1683676v1_genomic.fna/markers.fasta [2024-01-24 12:25:43,323] [INFO] Task started: Blastn [2024-01-24 12:25:43,323] [INFO] Running command: blastn -query GCF_016836765.1_ASM1683676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/reference_markers.fasta -out GCF_016836765.1_ASM1683676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:25:44,322] [INFO] Task succeeded: Blastn [2024-01-24 12:25:44,326] [INFO] Selected 12 target genomes. [2024-01-24 12:25:44,326] [INFO] Target genome list was writen to GCF_016836765.1_ASM1683676v1_genomic.fna/target_genomes.txt [2024-01-24 12:25:44,331] [INFO] Task started: fastANI [2024-01-24 12:25:44,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f9ab82-5a67-46ef-9c92-18c270d699cc/GCF_016836765.1_ASM1683676v1_genomic.fna.gz --refList GCF_016836765.1_ASM1683676v1_genomic.fna/target_genomes.txt --output GCF_016836765.1_ASM1683676v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:26:07,785] [INFO] Task succeeded: fastANI [2024-01-24 12:26:07,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:26:07,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:26:07,803] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold) [2024-01-24 12:26:07,803] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:26:07,803] [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 Burkholderia diffusa strain=DSM 23434 GCA_016836765.1 488732 488732 suspected-type True 100.0 2317 2322 95 conclusive Burkholderia diffusa GCA_902499115.1 488732 488732 suspected-type True 99.9953 2285 2322 95 conclusive Burkholderia diffusa strain=CCUG 54558 GCA_008802145.1 488732 488732 suspected-type True 99.8966 2093 2322 95 conclusive Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 93.8591 1861 2322 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 93.8407 1823 2322 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 91.9943 1791 2322 95 below_threshold Burkholderia cepacia strain=NBRC 14074 GCA_001528845.1 292 292 type True 90.9344 1858 2322 95 below_threshold Burkholderia cepacia strain=ATCC 25416 GCA_000473485.1 292 292 type True 90.916 1899 2322 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.5446 1621 2322 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.538 1676 2322 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.4499 1313 2322 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.6614 1085 2322 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:26:07,805] [INFO] DFAST Taxonomy check result was written to GCF_016836765.1_ASM1683676v1_genomic.fna/tc_result.tsv [2024-01-24 12:26:07,805] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:26:07,805] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:26:07,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/checkm_data [2024-01-24 12:26:07,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:26:07,871] [INFO] Task started: CheckM [2024-01-24 12:26:07,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016836765.1_ASM1683676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016836765.1_ASM1683676v1_genomic.fna/checkm_input GCF_016836765.1_ASM1683676v1_genomic.fna/checkm_result [2024-01-24 12:27:15,911] [INFO] Task succeeded: CheckM [2024-01-24 12:27:15,913] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:27:15,938] [INFO] ===== Completeness check finished ===== [2024-01-24 12:27:15,938] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:27:15,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016836765.1_ASM1683676v1_genomic.fna/markers.fasta) [2024-01-24 12:27:15,939] [INFO] Task started: Blastn [2024-01-24 12:27:15,939] [INFO] Running command: blastn -query GCF_016836765.1_ASM1683676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83edeab0-a3a5-4b83-9827-15f2091d90fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_016836765.1_ASM1683676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:27:17,886] [INFO] Task succeeded: Blastn [2024-01-24 12:27:17,889] [INFO] Selected 10 target genomes. [2024-01-24 12:27:17,889] [INFO] Target genome list was writen to GCF_016836765.1_ASM1683676v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:27:17,932] [INFO] Task started: fastANI [2024-01-24 12:27:17,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f9ab82-5a67-46ef-9c92-18c270d699cc/GCF_016836765.1_ASM1683676v1_genomic.fna.gz --refList GCF_016836765.1_ASM1683676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016836765.1_ASM1683676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:27:38,521] [INFO] Task succeeded: fastANI [2024-01-24 12:27:38,533] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:27:38,533] [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_902499115.1 s__Burkholderia diffusa 99.9953 2285 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 conclusive GCF_001718315.1 s__Burkholderia diffusa_B 94.3755 1927 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.43 98.33 0.91 0.89 12 - GCF_902833055.1 s__Burkholderia territorii 93.889 1858 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 - GCF_000949135.2 s__Burkholderia sp000949135 93.8282 1906 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_003853645.1 s__Burkholderia sp003853645 93.7396 1896 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_003853415.1 s__Burkholderia sp003853415 93.394 1870 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_001443045.1 s__Burkholderia ambifaria_A 93.0728 1870 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_000292915.1 s__Burkholderia cepacia_D 92.9676 1701 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001411495.1 s__Burkholderia cepacia 90.8946 1895 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.84 96.33 0.89 0.79 182 - GCF_001718835.1 s__Burkholderia cepacia_F 90.4907 1676 2322 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:27:38,535] [INFO] GTDB search result was written to GCF_016836765.1_ASM1683676v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:27:38,536] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:27:38,539] [INFO] DFAST_QC result json was written to GCF_016836765.1_ASM1683676v1_genomic.fna/dqc_result.json [2024-01-24 12:27:38,539] [INFO] DFAST_QC completed! [2024-01-24 12:27:38,539] [INFO] Total running time: 0h2m18s