[2024-01-24 11:20:34,399] [INFO] DFAST_QC pipeline started. [2024-01-24 11:20:34,401] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:20:34,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference [2024-01-24 11:20:35,596] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:20:35,597] [INFO] Task started: Prodigal [2024-01-24 11:20:35,597] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3ff85bb-feac-42d6-9fe7-8abe23355981/GCF_002097715.1_ASM209771v1_genomic.fna.gz | prodigal -d GCF_002097715.1_ASM209771v1_genomic.fna/cds.fna -a GCF_002097715.1_ASM209771v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:20:59,215] [INFO] Task succeeded: Prodigal [2024-01-24 11:20:59,216] [INFO] Task started: HMMsearch [2024-01-24 11:20:59,216] [INFO] Running command: hmmsearch --tblout GCF_002097715.1_ASM209771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/reference_markers.hmm GCF_002097715.1_ASM209771v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:20:59,566] [INFO] Task succeeded: HMMsearch [2024-01-24 11:20:59,567] [INFO] Found 6/6 markers. [2024-01-24 11:20:59,627] [INFO] Query marker FASTA was written to GCF_002097715.1_ASM209771v1_genomic.fna/markers.fasta [2024-01-24 11:20:59,627] [INFO] Task started: Blastn [2024-01-24 11:20:59,627] [INFO] Running command: blastn -query GCF_002097715.1_ASM209771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/reference_markers.fasta -out GCF_002097715.1_ASM209771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:21:00,570] [INFO] Task succeeded: Blastn [2024-01-24 11:21:00,574] [INFO] Selected 13 target genomes. [2024-01-24 11:21:00,575] [INFO] Target genome list was writen to GCF_002097715.1_ASM209771v1_genomic.fna/target_genomes.txt [2024-01-24 11:21:00,582] [INFO] Task started: fastANI [2024-01-24 11:21:00,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3ff85bb-feac-42d6-9fe7-8abe23355981/GCF_002097715.1_ASM209771v1_genomic.fna.gz --refList GCF_002097715.1_ASM209771v1_genomic.fna/target_genomes.txt --output GCF_002097715.1_ASM209771v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:21:27,605] [INFO] Task succeeded: fastANI [2024-01-24 11:21:27,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:21:27,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:21:27,627] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold) [2024-01-24 11:21:27,628] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:21:27,628] [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_002097715.1 265293 101571 type True 100.0 2609 2611 95 conclusive Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 99.9548 2497 2611 95 conclusive Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 94.8153 2036 2611 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 94.8001 2105 2611 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 91.2724 1923 2611 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 88.8872 1598 2611 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 88.3738 1625 2611 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 88.3046 1672 2611 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.8466 1372 2611 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.9779 1144 2611 95 below_threshold Caballeronia mineralivorans strain=PML1(12) GCA_001028175.1 2010198 2010198 type True 78.9381 777 2611 95 below_threshold Sphingomonas horti strain=MAH-20 GCA_009753715.1 2682842 2682842 type True 75.1899 218 2611 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:21:27,630] [INFO] DFAST Taxonomy check result was written to GCF_002097715.1_ASM209771v1_genomic.fna/tc_result.tsv [2024-01-24 11:21:27,630] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:21:27,631] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:21:27,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/checkm_data [2024-01-24 11:21:27,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:21:27,703] [INFO] Task started: CheckM [2024-01-24 11:21:27,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002097715.1_ASM209771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002097715.1_ASM209771v1_genomic.fna/checkm_input GCF_002097715.1_ASM209771v1_genomic.fna/checkm_result [2024-01-24 11:22:49,382] [INFO] Task succeeded: CheckM [2024-01-24 11:22:49,384] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:22:49,411] [INFO] ===== Completeness check finished ===== [2024-01-24 11:22:49,411] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:22:49,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002097715.1_ASM209771v1_genomic.fna/markers.fasta) [2024-01-24 11:22:49,412] [INFO] Task started: Blastn [2024-01-24 11:22:49,412] [INFO] Running command: blastn -query GCF_002097715.1_ASM209771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5096bb-370d-425f-a042-d5b289272302/dqc_reference/reference_markers_gtdb.fasta -out GCF_002097715.1_ASM209771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:22:51,112] [INFO] Task succeeded: Blastn [2024-01-24 11:22:51,116] [INFO] Selected 14 target genomes. [2024-01-24 11:22:51,116] [INFO] Target genome list was writen to GCF_002097715.1_ASM209771v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:22:51,130] [INFO] Task started: fastANI [2024-01-24 11:22:51,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3ff85bb-feac-42d6-9fe7-8abe23355981/GCF_002097715.1_ASM209771v1_genomic.fna.gz --refList GCF_002097715.1_ASM209771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002097715.1_ASM209771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:23:17,707] [INFO] Task succeeded: fastANI [2024-01-24 11:23:17,725] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:23:17,725] [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 100.0 2611 2611 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 94.6972 1994 2611 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 91.3192 1917 2611 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 91.251 1949 2611 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 90.4577 1705 2611 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 88.9194 1594 2611 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 88.7298 1730 2611 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCA_001883705.1 s__Burkholderia catarinensis 88.4836 1511 2611 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003853645.1 s__Burkholderia sp003853645 88.4672 1707 2611 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_902833055.1 s__Burkholderia territorii 88.3296 1630 2611 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 78.9298 779 2611 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 77.0387 161 2611 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 76.7087 483 2611 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Methylibium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 11:23:17,727] [INFO] GTDB search result was written to GCF_002097715.1_ASM209771v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:23:17,727] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:23:17,731] [INFO] DFAST_QC result json was written to GCF_002097715.1_ASM209771v1_genomic.fna/dqc_result.json [2024-01-24 11:23:17,731] [INFO] DFAST_QC completed! [2024-01-24 11:23:17,731] [INFO] Total running time: 0h2m43s