[2024-01-24 11:34:54,308] [INFO] DFAST_QC pipeline started. [2024-01-24 11:34:54,312] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:34:54,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference [2024-01-24 11:34:56,118] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:34:56,119] [INFO] Task started: Prodigal [2024-01-24 11:34:56,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d3d84a9-774c-40e5-8a1c-52a86e3bf380/GCF_022870505.1_ASM2287050v1_genomic.fna.gz | prodigal -d GCF_022870505.1_ASM2287050v1_genomic.fna/cds.fna -a GCF_022870505.1_ASM2287050v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:35:21,733] [INFO] Task succeeded: Prodigal [2024-01-24 11:35:21,734] [INFO] Task started: HMMsearch [2024-01-24 11:35:21,734] [INFO] Running command: hmmsearch --tblout GCF_022870505.1_ASM2287050v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/reference_markers.hmm GCF_022870505.1_ASM2287050v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:35:22,067] [INFO] Task succeeded: HMMsearch [2024-01-24 11:35:22,068] [INFO] Found 6/6 markers. [2024-01-24 11:35:22,124] [INFO] Query marker FASTA was written to GCF_022870505.1_ASM2287050v1_genomic.fna/markers.fasta [2024-01-24 11:35:22,124] [INFO] Task started: Blastn [2024-01-24 11:35:22,124] [INFO] Running command: blastn -query GCF_022870505.1_ASM2287050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/reference_markers.fasta -out GCF_022870505.1_ASM2287050v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:35:23,170] [INFO] Task succeeded: Blastn [2024-01-24 11:35:23,175] [INFO] Selected 13 target genomes. [2024-01-24 11:35:23,176] [INFO] Target genome list was writen to GCF_022870505.1_ASM2287050v1_genomic.fna/target_genomes.txt [2024-01-24 11:35:23,183] [INFO] Task started: fastANI [2024-01-24 11:35:23,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d3d84a9-774c-40e5-8a1c-52a86e3bf380/GCF_022870505.1_ASM2287050v1_genomic.fna.gz --refList GCF_022870505.1_ASM2287050v1_genomic.fna/target_genomes.txt --output GCF_022870505.1_ASM2287050v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:35:52,267] [INFO] Task succeeded: fastANI [2024-01-24 11:35:52,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:35:52,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:35:52,284] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold) [2024-01-24 11:35:52,284] [INFO] The taxonomy check result is classified as 'inconclusive'. [2024-01-24 11:35:52,284] [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 perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 100.0 2556 2556 95 inconclusive Burkholderia plantarii strain=ATCC 43733 GCA_001411805.1 41899 41899 type True 96.0141 2244 2556 95 inconclusive Burkholderia plantarii strain=LMG 9035 GCA_902832905.1 41899 41899 type True 95.9998 2216 2556 95 inconclusive Burkholderia glumae strain=ATCC 33617 GCA_000960995.1 337 337 type True 92.6528 1657 2556 95 below_threshold Burkholderia glumae strain=LMG 2196 GCA_902832765.1 337 337 type True 92.6165 1638 2556 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 83.7951 1349 2556 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 83.658 1399 2556 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 83.5957 1357 2556 95 below_threshold Paraburkholderia silviterrae strain=4M-K11 GCA_004353915.1 2528715 2528715 type True 81.1668 1091 2556 95 below_threshold Paraburkholderia piptadeniae strain=STM 7183 GCA_900007165.2 1701573 1701573 type True 80.8756 1029 2556 95 below_threshold Paraburkholderia franconis strain=CNPSo 3157 GCA_009362735.1 2654983 2654983 type True 80.6264 1061 2556 95 below_threshold Caballeronia pedi GCA_001544915.2 1777141 1777141 type True 80.1079 1080 2556 95 below_threshold Arhodomonas aquaeolei strain=DSM 8974 GCA_000374645.1 2369 2369 type True 75.6296 233 2556 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:35:52,286] [INFO] DFAST Taxonomy check result was written to GCF_022870505.1_ASM2287050v1_genomic.fna/tc_result.tsv [2024-01-24 11:35:52,286] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:35:52,286] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:35:52,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/checkm_data [2024-01-24 11:35:52,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:35:52,357] [INFO] Task started: CheckM [2024-01-24 11:35:52,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022870505.1_ASM2287050v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022870505.1_ASM2287050v1_genomic.fna/checkm_input GCF_022870505.1_ASM2287050v1_genomic.fna/checkm_result [2024-01-24 11:37:24,959] [INFO] Task succeeded: CheckM [2024-01-24 11:37:24,961] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:37:24,985] [INFO] ===== Completeness check finished ===== [2024-01-24 11:37:24,985] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:37:24,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022870505.1_ASM2287050v1_genomic.fna/markers.fasta) [2024-01-24 11:37:24,986] [INFO] Task started: Blastn [2024-01-24 11:37:24,986] [INFO] Running command: blastn -query GCF_022870505.1_ASM2287050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd743d9-9292-4ebd-95a6-716f156b762c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022870505.1_ASM2287050v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:37:26,880] [INFO] Task succeeded: Blastn [2024-01-24 11:37:26,885] [INFO] Selected 14 target genomes. [2024-01-24 11:37:26,885] [INFO] Target genome list was writen to GCF_022870505.1_ASM2287050v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:37:26,897] [INFO] Task started: fastANI [2024-01-24 11:37:26,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d3d84a9-774c-40e5-8a1c-52a86e3bf380/GCF_022870505.1_ASM2287050v1_genomic.fna.gz --refList GCF_022870505.1_ASM2287050v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022870505.1_ASM2287050v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:37:53,601] [INFO] Task succeeded: fastANI [2024-01-24 11:37:53,620] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:37:53,620] [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_001411805.1 s__Burkholderia plantarii 96.0126 2243 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.45 95.52 0.94 0.88 5 conclusive GCF_000960995.1 s__Burkholderia glumae 92.6515 1658 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.66 99.30 0.96 0.92 18 - GCA_009914575.1 s__Burkholderia gladioli_B 88.0385 418 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000959725.1 s__Burkholderia gladioli 87.4402 1843 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.34 97.08 0.90 0.82 265 - GCF_017104645.1 s__Burkholderia sp017104645 87.1797 1458 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000687455.2 s__Burkholderia sp000687455 83.8735 1055 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_013403875.1 s__Burkholderia guangdongensis 83.7628 1099 2556 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 83.7002 1401 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 - GCF_902833145.1 s__Burkholderia sp902833145 83.6502 1405 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_902833045.1 s__Burkholderia sp902833045 83.2181 1351 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.81 96.81 0.81 0.81 2 - GCF_000732615.1 s__Burkholderia paludis 83.1721 1405 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.34 99.33 0.95 0.95 4 - GCF_005280735.1 s__Trinickia sp005280735 81.4494 1072 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_014200455.1 s__Paraburkholderia bannensis_A 80.7677 1091 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.99 99.99 0.99 0.99 2 - GCF_003368325.1 s__Paraburkholderia caffeinilytica 80.3622 1066 2556 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 100.00 100.00 1.00 1.00 3 - -------------------------------------------------------------------------------- [2024-01-24 11:37:53,622] [INFO] GTDB search result was written to GCF_022870505.1_ASM2287050v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:37:53,622] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:37:53,626] [INFO] DFAST_QC result json was written to GCF_022870505.1_ASM2287050v1_genomic.fna/dqc_result.json [2024-01-24 11:37:53,626] [INFO] DFAST_QC completed! [2024-01-24 11:37:53,626] [INFO] Total running time: 0h2m59s