[2024-01-24 11:35:11,596] [INFO] DFAST_QC pipeline started. [2024-01-24 11:35:11,600] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:35:11,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference [2024-01-24 11:35:12,918] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:35:12,919] [INFO] Task started: Prodigal [2024-01-24 11:35:12,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgd38b5992-350e-4e0c-91b4-a859dbb53149/GCF_013403875.1_ASM1340387v1_genomic.fna.gz | prodigal -d GCF_013403875.1_ASM1340387v1_genomic.fna/cds.fna -a GCF_013403875.1_ASM1340387v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:35:29,273] [INFO] Task succeeded: Prodigal [2024-01-24 11:35:29,273] [INFO] Task started: HMMsearch [2024-01-24 11:35:29,273] [INFO] Running command: hmmsearch --tblout GCF_013403875.1_ASM1340387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/reference_markers.hmm GCF_013403875.1_ASM1340387v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:35:29,594] [INFO] Task succeeded: HMMsearch [2024-01-24 11:35:29,595] [INFO] Found 6/6 markers. [2024-01-24 11:35:29,644] [INFO] Query marker FASTA was written to GCF_013403875.1_ASM1340387v1_genomic.fna/markers.fasta [2024-01-24 11:35:29,644] [INFO] Task started: Blastn [2024-01-24 11:35:29,644] [INFO] Running command: blastn -query GCF_013403875.1_ASM1340387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/reference_markers.fasta -out GCF_013403875.1_ASM1340387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:35:30,596] [INFO] Task succeeded: Blastn [2024-01-24 11:35:30,599] [INFO] Selected 21 target genomes. [2024-01-24 11:35:30,599] [INFO] Target genome list was writen to GCF_013403875.1_ASM1340387v1_genomic.fna/target_genomes.txt [2024-01-24 11:35:30,604] [INFO] Task started: fastANI [2024-01-24 11:35:30,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgd38b5992-350e-4e0c-91b4-a859dbb53149/GCF_013403875.1_ASM1340387v1_genomic.fna.gz --refList GCF_013403875.1_ASM1340387v1_genomic.fna/target_genomes.txt --output GCF_013403875.1_ASM1340387v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:36:06,961] [INFO] Task succeeded: fastANI [2024-01-24 11:36:06,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:36:06,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:36:06,980] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:36:06,980] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:36:06,980] [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 strain=LMG 20358 GCA_902833085.1 101571 101571 type True 87.2803 1287 1910 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 87.2716 1249 1910 95 below_threshold Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002097715.1 265293 101571 type True 87.2575 1276 1910 95 below_threshold Burkholderia ubonensis subsp. mesacidophila strain=ATCC 31433 GCA_002362295.1 265293 101571 type True 87.2301 1247 1910 95 below_threshold Burkholderia stagnalis GCA_902499155.1 1503054 1503054 type True 87.1905 1218 1910 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 87.1571 1218 1910 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 87.1044 1278 1910 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 86.7329 1143 1910 95 below_threshold Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 86.6742 1193 1910 95 below_threshold Burkholderia multivorans strain=NCTC13007 GCA_900446205.1 87883 87883 type True 86.6642 1211 1910 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000959525.1 87883 87883 type True 86.6382 1196 1910 95 below_threshold Burkholderia dolosa strain=LMG 18943 GCA_902499135.1 152500 152500 type True 86.5657 1167 1910 95 below_threshold Burkholderia dolosa strain=FDAARGOS_1463 GCA_019930785.1 152500 152500 type True 86.5557 1218 1910 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000286555.1 87883 87883 type True 86.5064 1035 1910 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 86.5051 1207 1910 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 86.4518 1268 1910 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 86.4377 1231 1910 95 below_threshold Burkholderia arboris GCA_902499125.1 488730 488730 type True 86.3566 1275 1910 95 below_threshold Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 86.2388 902 1910 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7944 1113 1910 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 82.0015 997 1910 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:36:06,982] [INFO] DFAST Taxonomy check result was written to GCF_013403875.1_ASM1340387v1_genomic.fna/tc_result.tsv [2024-01-24 11:36:06,983] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:36:06,983] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:36:06,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/checkm_data [2024-01-24 11:36:06,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:36:07,046] [INFO] Task started: CheckM [2024-01-24 11:36:07,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013403875.1_ASM1340387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013403875.1_ASM1340387v1_genomic.fna/checkm_input GCF_013403875.1_ASM1340387v1_genomic.fna/checkm_result [2024-01-24 11:36:59,093] [INFO] Task succeeded: CheckM [2024-01-24 11:36:59,095] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:36:59,118] [INFO] ===== Completeness check finished ===== [2024-01-24 11:36:59,118] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:36:59,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013403875.1_ASM1340387v1_genomic.fna/markers.fasta) [2024-01-24 11:36:59,119] [INFO] Task started: Blastn [2024-01-24 11:36:59,119] [INFO] Running command: blastn -query GCF_013403875.1_ASM1340387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc02959cf-838a-4dd3-b799-fd5d186e4f05/dqc_reference/reference_markers_gtdb.fasta -out GCF_013403875.1_ASM1340387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:37:00,768] [INFO] Task succeeded: Blastn [2024-01-24 11:37:00,772] [INFO] Selected 16 target genomes. [2024-01-24 11:37:00,773] [INFO] Target genome list was writen to GCF_013403875.1_ASM1340387v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:37:00,820] [INFO] Task started: fastANI [2024-01-24 11:37:00,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgd38b5992-350e-4e0c-91b4-a859dbb53149/GCF_013403875.1_ASM1340387v1_genomic.fna.gz --refList GCF_013403875.1_ASM1340387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013403875.1_ASM1340387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:37:30,177] [INFO] Task succeeded: fastANI [2024-01-24 11:37:30,202] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:37:30,202] [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_013403875.1 s__Burkholderia guangdongensis 100.0 1908 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 conclusive GCF_000959245.1 s__Burkholderia ubonensis 87.5517 1256 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 - GCF_003854275.1 s__Burkholderia sp003854275 87.2177 1272 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_002097715.1 s__Burkholderia acidophila 87.2144 1279 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_902499075.1 s__Burkholderia pseudomultivorans 87.1657 1217 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_004343775.1 s__Burkholderia sp004343775 87.1622 1313 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902830275.1 s__Burkholderia stagnalis 87.1464 1274 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 - GCF_000687455.2 s__Burkholderia sp000687455 86.8803 1076 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000959525.1 s__Burkholderia multivorans 86.7008 1189 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.58 96.90 0.90 0.85 326 - GCF_001547525.1 s__Burkholderia anthina_A 86.6911 1239 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.44 98.20 0.94 0.91 13 - GCF_902499045.1 s__Burkholderia latens 86.6857 1192 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_902499135.1 s__Burkholderia dolosa 86.6796 1155 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.52 98.66 0.97 0.91 15 - GCF_003853415.1 s__Burkholderia sp003853415 86.53 1279 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_902833055.1 s__Burkholderia territorii 86.4254 1233 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 - GCF_902499125.1 s__Burkholderia arboris 86.3923 1270 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.82 96.20 0.94 0.91 3 - GCA_018375725.1 s__Burkholderia sp018375725 86.1597 849 1910 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 11:37:30,204] [INFO] GTDB search result was written to GCF_013403875.1_ASM1340387v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:37:30,205] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:37:30,209] [INFO] DFAST_QC result json was written to GCF_013403875.1_ASM1340387v1_genomic.fna/dqc_result.json [2024-01-24 11:37:30,209] [INFO] DFAST_QC completed! [2024-01-24 11:37:30,209] [INFO] Total running time: 0h2m19s