[2024-01-25 18:20:20,767] [INFO] DFAST_QC pipeline started. [2024-01-25 18:20:20,769] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:20:20,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference [2024-01-25 18:20:21,902] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:20:21,902] [INFO] Task started: Prodigal [2024-01-25 18:20:21,902] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0920411-8fd8-4e49-b237-fd1bbba1beb0/GCF_902499045.1_ASM90249904v1_genomic.fna.gz | prodigal -d GCF_902499045.1_ASM90249904v1_genomic.fna/cds.fna -a GCF_902499045.1_ASM90249904v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:20:40,295] [INFO] Task succeeded: Prodigal [2024-01-25 18:20:40,295] [INFO] Task started: HMMsearch [2024-01-25 18:20:40,295] [INFO] Running command: hmmsearch --tblout GCF_902499045.1_ASM90249904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/reference_markers.hmm GCF_902499045.1_ASM90249904v1_genomic.fna/protein.faa > /dev/null [2024-01-25 18:20:40,575] [INFO] Task succeeded: HMMsearch [2024-01-25 18:20:40,576] [INFO] Found 6/6 markers. [2024-01-25 18:20:40,627] [INFO] Query marker FASTA was written to GCF_902499045.1_ASM90249904v1_genomic.fna/markers.fasta [2024-01-25 18:20:40,628] [INFO] Task started: Blastn [2024-01-25 18:20:40,628] [INFO] Running command: blastn -query GCF_902499045.1_ASM90249904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/reference_markers.fasta -out GCF_902499045.1_ASM90249904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:20:41,603] [INFO] Task succeeded: Blastn [2024-01-25 18:20:41,606] [INFO] Selected 18 target genomes. [2024-01-25 18:20:41,606] [INFO] Target genome list was writen to GCF_902499045.1_ASM90249904v1_genomic.fna/target_genomes.txt [2024-01-25 18:20:41,619] [INFO] Task started: fastANI [2024-01-25 18:20:41,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0920411-8fd8-4e49-b237-fd1bbba1beb0/GCF_902499045.1_ASM90249904v1_genomic.fna.gz --refList GCF_902499045.1_ASM90249904v1_genomic.fna/target_genomes.txt --output GCF_902499045.1_ASM90249904v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:21:15,825] [INFO] Task succeeded: fastANI [2024-01-25 18:21:15,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:21:15,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:21:15,838] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold) [2024-01-25 18:21:15,839] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 18:21:15,839] [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 latens GCA_902499045.1 488446 488446 suspected-type True 100.0 2287 2298 95 conclusive Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 99.9591 2193 2298 95 conclusive Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 91.9223 1827 2298 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000959545.1 152480 152480 type True 91.9004 1833 2298 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 91.6024 1758 2298 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 91.5977 1734 2298 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 91.2818 1702 2298 95 below_threshold Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 91.0936 1219 2298 95 below_threshold Burkholderia cenocepacia strain=NCTC13227 GCA_900446215.1 95486 95486 type True 90.7321 1762 2298 95 below_threshold Burkholderia vietnamiensis strain=LMG 10929 GCA_902830295.1 60552 60552 type True 90.5386 1639 2298 95 below_threshold Burkholderia vietnamiensis strain=LMG 10929 GCA_000959445.1 60552 60552 type True 90.5223 1648 2298 95 below_threshold Burkholderia vietnamiensis strain=FDAARGOS_1488 GCA_020099355.1 60552 60552 type True 90.5031 1642 2298 95 below_threshold Burkholderia pyrrocinia strain=LMG 14191 GCA_902832895.1 60550 60550 suspected-type True 90.4991 1762 2298 95 below_threshold Burkholderia pyrrocinia strain=DSM 10685 GCA_001028665.1 60550 60550 suspected-type True 90.47 1766 2298 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.3754 1601 2298 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.3401 1636 2298 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.4659 1295 2298 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.605 1100 2298 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:21:15,840] [INFO] DFAST Taxonomy check result was written to GCF_902499045.1_ASM90249904v1_genomic.fna/tc_result.tsv [2024-01-25 18:21:15,840] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:21:15,841] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:21:15,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/checkm_data [2024-01-25 18:21:15,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:21:15,909] [INFO] Task started: CheckM [2024-01-25 18:21:15,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499045.1_ASM90249904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499045.1_ASM90249904v1_genomic.fna/checkm_input GCF_902499045.1_ASM90249904v1_genomic.fna/checkm_result [2024-01-25 18:22:24,955] [INFO] Task succeeded: CheckM [2024-01-25 18:22:24,956] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:22:24,977] [INFO] ===== Completeness check finished ===== [2024-01-25 18:22:24,978] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:22:24,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499045.1_ASM90249904v1_genomic.fna/markers.fasta) [2024-01-25 18:22:24,979] [INFO] Task started: Blastn [2024-01-25 18:22:24,979] [INFO] Running command: blastn -query GCF_902499045.1_ASM90249904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68f107e5-68e3-4c5a-a8a9-e06d69f67693/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499045.1_ASM90249904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:22:26,971] [INFO] Task succeeded: Blastn [2024-01-25 18:22:26,974] [INFO] Selected 12 target genomes. [2024-01-25 18:22:26,974] [INFO] Target genome list was writen to GCF_902499045.1_ASM90249904v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:22:26,989] [INFO] Task started: fastANI [2024-01-25 18:22:26,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0920411-8fd8-4e49-b237-fd1bbba1beb0/GCF_902499045.1_ASM90249904v1_genomic.fna.gz --refList GCF_902499045.1_ASM90249904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499045.1_ASM90249904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:22:51,672] [INFO] Task succeeded: fastANI [2024-01-25 18:22:51,680] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:22:51,680] [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_902499045.1 s__Burkholderia latens 100.0 2287 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 conclusive GCF_001718795.1 s__Burkholderia latens_A 92.9098 1796 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.33 99.18 0.94 0.92 8 - GCF_000949135.2 s__Burkholderia sp000949135 92.2369 1801 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_003853415.1 s__Burkholderia sp003853415 92.208 1781 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_003853645.1 s__Burkholderia sp003853645 91.9855 1756 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_000292915.1 s__Burkholderia cepacia_D 91.9376 1594 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000203915.1 s__Burkholderia ambifaria 91.9196 1828 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.41 95.73 0.89 0.79 83 - GCF_001443045.1 s__Burkholderia ambifaria_A 91.7797 1752 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_902833055.1 s__Burkholderia territorii 91.601 1757 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 - GCF_001718315.1 s__Burkholderia diffusa_B 91.5777 1752 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.43 98.33 0.91 0.89 12 - GCF_902833145.1 s__Burkholderia sp902833145 90.9998 1783 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_900446215.1 s__Burkholderia cenocepacia 90.8182 1752 2298 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - -------------------------------------------------------------------------------- [2024-01-25 18:22:51,681] [INFO] GTDB search result was written to GCF_902499045.1_ASM90249904v1_genomic.fna/result_gtdb.tsv [2024-01-25 18:22:51,682] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:22:51,686] [INFO] DFAST_QC result json was written to GCF_902499045.1_ASM90249904v1_genomic.fna/dqc_result.json [2024-01-25 18:22:51,687] [INFO] DFAST_QC completed! [2024-01-25 18:22:51,687] [INFO] Total running time: 0h2m31s