[2024-01-25 17:48:35,790] [INFO] DFAST_QC pipeline started. [2024-01-25 17:48:35,791] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 17:48:35,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference [2024-01-25 17:48:36,897] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 17:48:36,897] [INFO] Task started: Prodigal [2024-01-25 17:48:36,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgad53f7ef-b312-4cbf-a8ad-c0d0b204972d/GCF_002362295.1_ASM236229v1_genomic.fna.gz | prodigal -d GCF_002362295.1_ASM236229v1_genomic.fna/cds.fna -a GCF_002362295.1_ASM236229v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 17:48:56,365] [INFO] Task succeeded: Prodigal [2024-01-25 17:48:56,366] [INFO] Task started: HMMsearch [2024-01-25 17:48:56,366] [INFO] Running command: hmmsearch --tblout GCF_002362295.1_ASM236229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/reference_markers.hmm GCF_002362295.1_ASM236229v1_genomic.fna/protein.faa > /dev/null [2024-01-25 17:48:56,693] [INFO] Task succeeded: HMMsearch [2024-01-25 17:48:56,694] [INFO] Found 6/6 markers. [2024-01-25 17:48:56,752] [INFO] Query marker FASTA was written to GCF_002362295.1_ASM236229v1_genomic.fna/markers.fasta [2024-01-25 17:48:56,752] [INFO] Task started: Blastn [2024-01-25 17:48:56,752] [INFO] Running command: blastn -query GCF_002362295.1_ASM236229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/reference_markers.fasta -out GCF_002362295.1_ASM236229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 17:48:57,644] [INFO] Task succeeded: Blastn [2024-01-25 17:48:57,647] [INFO] Selected 13 target genomes. [2024-01-25 17:48:57,647] [INFO] Target genome list was writen to GCF_002362295.1_ASM236229v1_genomic.fna/target_genomes.txt [2024-01-25 17:48:57,658] [INFO] Task started: fastANI [2024-01-25 17:48:57,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgad53f7ef-b312-4cbf-a8ad-c0d0b204972d/GCF_002362295.1_ASM236229v1_genomic.fna.gz --refList GCF_002362295.1_ASM236229v1_genomic.fna/target_genomes.txt --output GCF_002362295.1_ASM236229v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 17:49:23,811] [INFO] Task succeeded: fastANI [2024-01-25 17:49:23,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 17:49:23,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 17:49:23,821] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold) [2024-01-25 17:49:23,821] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 17:49:23,821] [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 subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 100.0 2500 2507 95 conclusive Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002097715.1 265293 101571 type True 99.9973 2505 2507 95 conclusive Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 94.7964 2050 2507 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 94.7826 2000 2507 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 91.2097 1868 2507 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 88.8123 1562 2507 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 88.344 1641 2507 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 88.3119 1584 2507 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.8864 1316 2507 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.9393 1112 2507 95 below_threshold Caballeronia mineralivorans strain=PML1(12) GCA_001028175.1 2010198 2010198 type True 78.968 742 2507 95 below_threshold Sphingomonas horti strain=MAH-20 GCA_009753715.1 2682842 2682842 type True 75.2378 188 2507 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 17:49:23,822] [INFO] DFAST Taxonomy check result was written to GCF_002362295.1_ASM236229v1_genomic.fna/tc_result.tsv [2024-01-25 17:49:23,823] [INFO] ===== Taxonomy check completed ===== [2024-01-25 17:49:23,823] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 17:49:23,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/checkm_data [2024-01-25 17:49:23,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 17:49:23,897] [INFO] Task started: CheckM [2024-01-25 17:49:23,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002362295.1_ASM236229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002362295.1_ASM236229v1_genomic.fna/checkm_input GCF_002362295.1_ASM236229v1_genomic.fna/checkm_result [2024-01-25 17:50:27,648] [INFO] Task succeeded: CheckM [2024-01-25 17:50:27,651] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 17:50:27,705] [INFO] ===== Completeness check finished ===== [2024-01-25 17:50:27,706] [INFO] ===== Start GTDB Search ===== [2024-01-25 17:50:27,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002362295.1_ASM236229v1_genomic.fna/markers.fasta) [2024-01-25 17:50:27,707] [INFO] Task started: Blastn [2024-01-25 17:50:27,707] [INFO] Running command: blastn -query GCF_002362295.1_ASM236229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a420d06-2fa5-4994-bc34-1d4c6c21b95f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002362295.1_ASM236229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 17:50:29,448] [INFO] Task succeeded: Blastn [2024-01-25 17:50:29,451] [INFO] Selected 14 target genomes. [2024-01-25 17:50:29,451] [INFO] Target genome list was writen to GCF_002362295.1_ASM236229v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 17:50:29,466] [INFO] Task started: fastANI [2024-01-25 17:50:29,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgad53f7ef-b312-4cbf-a8ad-c0d0b204972d/GCF_002362295.1_ASM236229v1_genomic.fna.gz --refList GCF_002362295.1_ASM236229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002362295.1_ASM236229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 17:50:56,819] [INFO] Task succeeded: fastANI [2024-01-25 17:50:56,832] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 17:50:56,832] [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_002097715.1 s__Burkholderia acidophila 99.9973 2505 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 conclusive GCF_000959245.1 s__Burkholderia ubonensis 94.6122 1938 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 - GCF_902830275.1 s__Burkholderia stagnalis 91.2221 1866 2507 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 91.0765 1900 2507 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 90.5316 1653 2507 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 88.811 1562 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_000949135.2 s__Burkholderia sp000949135 88.7674 1671 2507 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 88.6095 1644 2507 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 88.5387 1478 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902833055.1 s__Burkholderia territorii 88.2923 1586 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 - GCF_001028175.1 s__Caballeronia mineralivorans 78.983 739 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.87 95.86 0.82 0.81 4 - GCA_012729605.1 s__Brachymonas sp012729605 76.9402 162 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas 95.0 N/A N/A N/A N/A 1 - GCA_902826655.1 s__Methylibium sp902826655 76.6973 464 2507 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 17:50:56,833] [INFO] GTDB search result was written to GCF_002362295.1_ASM236229v1_genomic.fna/result_gtdb.tsv [2024-01-25 17:50:56,835] [INFO] ===== GTDB Search completed ===== [2024-01-25 17:50:56,838] [INFO] DFAST_QC result json was written to GCF_002362295.1_ASM236229v1_genomic.fna/dqc_result.json [2024-01-25 17:50:56,838] [INFO] DFAST_QC completed! [2024-01-25 17:50:56,838] [INFO] Total running time: 0h2m21s