[2024-01-24 13:18:41,108] [INFO] DFAST_QC pipeline started. [2024-01-24 13:18:41,110] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:18:41,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference [2024-01-24 13:18:42,508] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:18:42,509] [INFO] Task started: Prodigal [2024-01-24 13:18:42,509] [INFO] Running command: gunzip -c /var/lib/cwl/stge23580d7-b673-4611-b843-e3d528daa046/GCF_902499185.1_ASM90249918v1_genomic.fna.gz | prodigal -d GCF_902499185.1_ASM90249918v1_genomic.fna/cds.fna -a GCF_902499185.1_ASM90249918v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:19:05,909] [INFO] Task succeeded: Prodigal [2024-01-24 13:19:05,909] [INFO] Task started: HMMsearch [2024-01-24 13:19:05,910] [INFO] Running command: hmmsearch --tblout GCF_902499185.1_ASM90249918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/reference_markers.hmm GCF_902499185.1_ASM90249918v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:19:06,356] [INFO] Task succeeded: HMMsearch [2024-01-24 13:19:06,358] [INFO] Found 6/6 markers. [2024-01-24 13:19:06,425] [INFO] Query marker FASTA was written to GCF_902499185.1_ASM90249918v1_genomic.fna/markers.fasta [2024-01-24 13:19:06,425] [INFO] Task started: Blastn [2024-01-24 13:19:06,425] [INFO] Running command: blastn -query GCF_902499185.1_ASM90249918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/reference_markers.fasta -out GCF_902499185.1_ASM90249918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:19:07,501] [INFO] Task succeeded: Blastn [2024-01-24 13:19:07,505] [INFO] Selected 9 target genomes. [2024-01-24 13:19:07,506] [INFO] Target genome list was writen to GCF_902499185.1_ASM90249918v1_genomic.fna/target_genomes.txt [2024-01-24 13:19:07,509] [INFO] Task started: fastANI [2024-01-24 13:19:07,510] [INFO] Running command: fastANI --query /var/lib/cwl/stge23580d7-b673-4611-b843-e3d528daa046/GCF_902499185.1_ASM90249918v1_genomic.fna.gz --refList GCF_902499185.1_ASM90249918v1_genomic.fna/target_genomes.txt --output GCF_902499185.1_ASM90249918v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:19:29,740] [INFO] Task succeeded: fastANI [2024-01-24 13:19:29,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:19:29,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:19:29,749] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:19:29,750] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:19:29,750] [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 ubonensis GCA_902499185.1 101571 101571 type True 100.0 2479 2486 95 conclusive Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 99.9927 2481 2486 95 conclusive Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002097715.1 265293 101571 type True 94.6798 2054 2486 95 below_threshold Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 94.6747 2015 2486 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 91.3074 1895 2486 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 89.0326 1564 2486 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 88.3938 1648 2486 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7895 1357 2486 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.9647 1119 2486 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:19:29,752] [INFO] DFAST Taxonomy check result was written to GCF_902499185.1_ASM90249918v1_genomic.fna/tc_result.tsv [2024-01-24 13:19:29,752] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:19:29,752] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:19:29,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/checkm_data [2024-01-24 13:19:29,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:19:29,828] [INFO] Task started: CheckM [2024-01-24 13:19:29,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499185.1_ASM90249918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499185.1_ASM90249918v1_genomic.fna/checkm_input GCF_902499185.1_ASM90249918v1_genomic.fna/checkm_result [2024-01-24 13:20:45,359] [INFO] Task succeeded: CheckM [2024-01-24 13:20:45,360] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:20:45,385] [INFO] ===== Completeness check finished ===== [2024-01-24 13:20:45,386] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:20:45,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499185.1_ASM90249918v1_genomic.fna/markers.fasta) [2024-01-24 13:20:45,386] [INFO] Task started: Blastn [2024-01-24 13:20:45,387] [INFO] Running command: blastn -query GCF_902499185.1_ASM90249918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7703cc-b5aa-43ac-a508-b50452cf7a43/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499185.1_ASM90249918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:20:47,549] [INFO] Task succeeded: Blastn [2024-01-24 13:20:47,554] [INFO] Selected 9 target genomes. [2024-01-24 13:20:47,555] [INFO] Target genome list was writen to GCF_902499185.1_ASM90249918v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:20:47,565] [INFO] Task started: fastANI [2024-01-24 13:20:47,565] [INFO] Running command: fastANI --query /var/lib/cwl/stge23580d7-b673-4611-b843-e3d528daa046/GCF_902499185.1_ASM90249918v1_genomic.fna.gz --refList GCF_902499185.1_ASM90249918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499185.1_ASM90249918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:21:09,706] [INFO] Task succeeded: fastANI [2024-01-24 13:21:09,723] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:21:09,723] [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_000959245.1 s__Burkholderia ubonensis 96.4625 2058 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 conclusive GCF_002097715.1 s__Burkholderia acidophila 94.7192 2050 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_902830275.1 s__Burkholderia stagnalis 91.2934 1897 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 - GCF_004343775.1 s__Burkholderia sp004343775 91.0512 1905 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003854275.1 s__Burkholderia sp003854275 90.3618 1702 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_902499075.1 s__Burkholderia pseudomultivorans 89.049 1562 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_003853645.1 s__Burkholderia sp003853645 88.6846 1678 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCA_001883705.1 s__Burkholderia catarinensis 88.5432 1564 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499115.1 s__Burkholderia diffusa 88.3984 1642 2486 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 - -------------------------------------------------------------------------------- [2024-01-24 13:21:09,725] [INFO] GTDB search result was written to GCF_902499185.1_ASM90249918v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:21:09,726] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:21:09,731] [INFO] DFAST_QC result json was written to GCF_902499185.1_ASM90249918v1_genomic.fna/dqc_result.json [2024-01-24 13:21:09,731] [INFO] DFAST_QC completed! [2024-01-24 13:21:09,731] [INFO] Total running time: 0h2m29s