[2024-01-24 12:53:36,076] [INFO] DFAST_QC pipeline started. [2024-01-24 12:53:36,078] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:53:36,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference [2024-01-24 12:53:37,384] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:53:37,385] [INFO] Task started: Prodigal [2024-01-24 12:53:37,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg3338b7bc-eec2-4c03-b2ac-0840cf55c498/GCF_008802125.1_ASM880212v1_genomic.fna.gz | prodigal -d GCF_008802125.1_ASM880212v1_genomic.fna/cds.fna -a GCF_008802125.1_ASM880212v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:54:00,175] [INFO] Task succeeded: Prodigal [2024-01-24 12:54:00,176] [INFO] Task started: HMMsearch [2024-01-24 12:54:00,176] [INFO] Running command: hmmsearch --tblout GCF_008802125.1_ASM880212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/reference_markers.hmm GCF_008802125.1_ASM880212v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:54:00,542] [INFO] Task succeeded: HMMsearch [2024-01-24 12:54:00,544] [INFO] Found 6/6 markers. [2024-01-24 12:54:00,609] [INFO] Query marker FASTA was written to GCF_008802125.1_ASM880212v1_genomic.fna/markers.fasta [2024-01-24 12:54:00,610] [INFO] Task started: Blastn [2024-01-24 12:54:00,610] [INFO] Running command: blastn -query GCF_008802125.1_ASM880212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/reference_markers.fasta -out GCF_008802125.1_ASM880212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:54:01,669] [INFO] Task succeeded: Blastn [2024-01-24 12:54:01,672] [INFO] Selected 12 target genomes. [2024-01-24 12:54:01,673] [INFO] Target genome list was writen to GCF_008802125.1_ASM880212v1_genomic.fna/target_genomes.txt [2024-01-24 12:54:01,684] [INFO] Task started: fastANI [2024-01-24 12:54:01,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg3338b7bc-eec2-4c03-b2ac-0840cf55c498/GCF_008802125.1_ASM880212v1_genomic.fna.gz --refList GCF_008802125.1_ASM880212v1_genomic.fna/target_genomes.txt --output GCF_008802125.1_ASM880212v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:54:29,145] [INFO] Task succeeded: fastANI [2024-01-24 12:54:29,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:54:29,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:54:29,162] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold) [2024-01-24 12:54:29,162] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:54:29,162] [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 stagnalis strain=CCUG 65686 GCA_008802125.1 1503054 1503054 type True 100.0 2573 2580 95 conclusive Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 99.9892 2560 2580 95 conclusive Burkholderia stagnalis GCA_902499155.1 1503054 1503054 type True 99.9494 2441 2580 95 conclusive Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002097715.1 265293 101571 type True 91.3357 1871 2580 95 below_threshold Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 91.3218 1816 2580 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 91.3216 1909 2580 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 91.3212 1861 2580 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_001758385.2 488447 488447 type True 88.6903 1786 2580 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 88.6902 1652 2580 95 below_threshold Burkholderia contaminans strain=LMG 23361 GCA_000987075.1 488447 488447 type True 88.6328 1792 2580 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.8175 1366 2580 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.9304 1112 2580 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:54:29,164] [INFO] DFAST Taxonomy check result was written to GCF_008802125.1_ASM880212v1_genomic.fna/tc_result.tsv [2024-01-24 12:54:29,164] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:54:29,165] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:54:29,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/checkm_data [2024-01-24 12:54:29,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:54:29,243] [INFO] Task started: CheckM [2024-01-24 12:54:29,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802125.1_ASM880212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802125.1_ASM880212v1_genomic.fna/checkm_input GCF_008802125.1_ASM880212v1_genomic.fna/checkm_result [2024-01-24 12:55:48,672] [INFO] Task succeeded: CheckM [2024-01-24 12:55:48,674] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:55:48,700] [INFO] ===== Completeness check finished ===== [2024-01-24 12:55:48,700] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:55:48,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802125.1_ASM880212v1_genomic.fna/markers.fasta) [2024-01-24 12:55:48,701] [INFO] Task started: Blastn [2024-01-24 12:55:48,701] [INFO] Running command: blastn -query GCF_008802125.1_ASM880212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d8b1ef-c787-4c81-996f-97cc3f716f74/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802125.1_ASM880212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:55:50,737] [INFO] Task succeeded: Blastn [2024-01-24 12:55:50,741] [INFO] Selected 10 target genomes. [2024-01-24 12:55:50,741] [INFO] Target genome list was writen to GCF_008802125.1_ASM880212v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:55:50,749] [INFO] Task started: fastANI [2024-01-24 12:55:50,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg3338b7bc-eec2-4c03-b2ac-0840cf55c498/GCF_008802125.1_ASM880212v1_genomic.fna.gz --refList GCF_008802125.1_ASM880212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802125.1_ASM880212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:56:13,982] [INFO] Task succeeded: fastANI [2024-01-24 12:56:13,994] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:56:13,994] [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_902830275.1 s__Burkholderia stagnalis 99.9892 2560 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 conclusive GCF_004343775.1 s__Burkholderia sp004343775 93.7944 2038 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000959245.1 s__Burkholderia ubonensis 91.442 1837 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 - GCF_002097715.1 s__Burkholderia acidophila 91.2733 1878 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_003854275.1 s__Burkholderia sp003854275 89.9832 1694 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_003853705.1 s__Burkholderia sp003853705 88.8683 1760 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_016899425.1 s__Burkholderia sp002223185 88.6997 1740 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_902499125.1 s__Burkholderia arboris 88.6894 1737 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCF_000987075.1 s__Burkholderia contaminans 88.6537 1788 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.97 95.20 0.90 0.82 86 - GCF_902833045.1 s__Burkholderia sp902833045 88.5445 1720 2580 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.81 96.81 0.81 0.81 2 - -------------------------------------------------------------------------------- [2024-01-24 12:56:13,996] [INFO] GTDB search result was written to GCF_008802125.1_ASM880212v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:56:13,996] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:56:13,999] [INFO] DFAST_QC result json was written to GCF_008802125.1_ASM880212v1_genomic.fna/dqc_result.json [2024-01-24 12:56:13,999] [INFO] DFAST_QC completed! [2024-01-24 12:56:13,999] [INFO] Total running time: 0h2m38s