[2024-01-24 11:27:19,125] [INFO] DFAST_QC pipeline started. [2024-01-24 11:27:19,126] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:27:19,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference [2024-01-24 11:27:20,289] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:27:20,290] [INFO] Task started: Prodigal [2024-01-24 11:27:20,290] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0d132fd-095a-4092-98ff-7a5eaf665e0e/GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna.gz | prodigal -d GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/cds.fna -a GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:27:42,225] [INFO] Task succeeded: Prodigal [2024-01-24 11:27:42,226] [INFO] Task started: HMMsearch [2024-01-24 11:27:42,226] [INFO] Running command: hmmsearch --tblout GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/reference_markers.hmm GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/protein.faa > /dev/null [2024-01-24 11:27:42,571] [INFO] Task succeeded: HMMsearch [2024-01-24 11:27:42,573] [INFO] Found 6/6 markers. [2024-01-24 11:27:42,628] [INFO] Query marker FASTA was written to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/markers.fasta [2024-01-24 11:27:42,628] [INFO] Task started: Blastn [2024-01-24 11:27:42,628] [INFO] Running command: blastn -query GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/reference_markers.fasta -out GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:27:43,406] [INFO] Task succeeded: Blastn [2024-01-24 11:27:43,409] [INFO] Selected 16 target genomes. [2024-01-24 11:27:43,409] [INFO] Target genome list was writen to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/target_genomes.txt [2024-01-24 11:27:43,431] [INFO] Task started: fastANI [2024-01-24 11:27:43,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d132fd-095a-4092-98ff-7a5eaf665e0e/GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna.gz --refList GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/target_genomes.txt --output GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:28:07,852] [INFO] Task succeeded: fastANI [2024-01-24 11:28:07,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:28:07,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:28:07,865] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:28:07,865] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:28:07,866] [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 Caballeronia mineralivorans strain=PML1(12) GCA_001028175.1 2010198 2010198 type True 83.746 1328 2257 95 below_threshold Caballeronia udeis GCA_001544555.2 1232866 1232866 type True 83.3427 1349 2257 95 below_threshold Caballeronia choica GCA_001544535.2 326476 326476 type True 81.0482 961 2257 95 below_threshold Caballeronia telluris GCA_001544495.2 326475 326475 type True 80.8676 996 2257 95 below_threshold Caballeronia glathei strain=LMG 14190 GCA_000751215.2 60547 60547 type True 80.8501 1003 2257 95 below_threshold Caballeronia arationis GCA_001544975.2 1777142 1777142 type True 80.8303 981 2257 95 below_threshold Caballeronia glathei strain=DSM 50014 GCA_000698595.1 60547 60547 type True 80.8137 1006 2257 95 below_threshold Caballeronia terrestris GCA_001544515.2 1226301 1226301 type True 80.8101 999 2257 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 79.8074 744 2257 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 79.5531 738 2257 95 below_threshold Paraburkholderia panacisoli strain=DCY113 GCA_008369935.1 2603818 2603818 type True 79.5517 823 2257 95 below_threshold Paraburkholderia kirstenboschensis strain=KB15 GCA_001636975.1 1245436 1245436 type True 79.404 653 2257 95 below_threshold Paraburkholderia elongata strain=5N GCA_013177735.1 2675747 2675747 type True 79.3481 779 2257 95 below_threshold Paraburkholderia madseniana strain=RP11 GCA_009690905.1 2599607 2599607 type True 79.1982 816 2257 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 79.1576 784 2257 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 79.1057 844 2257 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:28:07,867] [INFO] DFAST Taxonomy check result was written to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/tc_result.tsv [2024-01-24 11:28:07,868] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:28:07,868] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:28:07,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/checkm_data [2024-01-24 11:28:07,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:28:07,933] [INFO] Task started: CheckM [2024-01-24 11:28:07,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/checkm_input GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/checkm_result [2024-01-24 11:29:08,903] [INFO] Task succeeded: CheckM [2024-01-24 11:29:08,904] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:29:08,927] [INFO] ===== Completeness check finished ===== [2024-01-24 11:29:08,927] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:29:08,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/markers.fasta) [2024-01-24 11:29:08,928] [INFO] Task started: Blastn [2024-01-24 11:29:08,928] [INFO] Running command: blastn -query GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ca33cf-5b18-4d75-b036-53c4287ce838/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:29:10,106] [INFO] Task succeeded: Blastn [2024-01-24 11:29:10,109] [INFO] Selected 9 target genomes. [2024-01-24 11:29:10,110] [INFO] Target genome list was writen to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:29:10,117] [INFO] Task started: fastANI [2024-01-24 11:29:10,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d132fd-095a-4092-98ff-7a5eaf665e0e/GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna.gz --refList GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/target_genomes_gtdb.txt --output GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:29:26,736] [INFO] Task succeeded: fastANI [2024-01-24 11:29:26,749] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:29:26,749] [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_001544455.2 s__Caballeronia sordidicola_B 100.0 2254 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 conclusive GCF_018449635.1 s__Caballeronia sp018449635 87.1514 1616 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001424345.1 s__Caballeronia sp001424345 86.8317 1559 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001557535.2 s__Caballeronia sp001557535 86.6832 1630 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.54 97.94 0.87 0.85 5 - GCF_001028175.1 s__Caballeronia mineralivorans 83.7499 1326 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.87 95.86 0.82 0.81 4 - GCF_018449515.1 s__Caballeronia sp018449515 83.5197 1422 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_002220365.1 s__Caballeronia sordidicola_C 83.3662 1353 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544555.2 s__Caballeronia udeis 83.3385 1350 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.62 95.53 0.77 0.76 8 - GCF_011493005.1 s__Caballeronia sp011493005 83.3082 1366 2257 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.62 99.62 0.93 0.93 2 - -------------------------------------------------------------------------------- [2024-01-24 11:29:26,751] [INFO] GTDB search result was written to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/result_gtdb.tsv [2024-01-24 11:29:26,751] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:29:26,754] [INFO] DFAST_QC result json was written to GCF_001544455.2_Burkholderia_sordidicola_LMG_22029_genomic.fna/dqc_result.json [2024-01-24 11:29:26,755] [INFO] DFAST_QC completed! [2024-01-24 11:29:26,755] [INFO] Total running time: 0h2m8s