[2024-01-24 11:35:13,285] [INFO] DFAST_QC pipeline started. [2024-01-24 11:35:13,287] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:35:13,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference [2024-01-24 11:35:14,484] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:35:14,485] [INFO] Task started: Prodigal [2024-01-24 11:35:14,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg899985fc-6f0d-482e-8501-4dc6ef5fdf27/GCF_000959445.1_ASM95944v1_genomic.fna.gz | prodigal -d GCF_000959445.1_ASM95944v1_genomic.fna/cds.fna -a GCF_000959445.1_ASM95944v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:35:37,031] [INFO] Task succeeded: Prodigal [2024-01-24 11:35:37,031] [INFO] Task started: HMMsearch [2024-01-24 11:35:37,031] [INFO] Running command: hmmsearch --tblout GCF_000959445.1_ASM95944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/reference_markers.hmm GCF_000959445.1_ASM95944v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:35:37,442] [INFO] Task succeeded: HMMsearch [2024-01-24 11:35:37,444] [INFO] Found 6/6 markers. [2024-01-24 11:35:37,496] [INFO] Query marker FASTA was written to GCF_000959445.1_ASM95944v1_genomic.fna/markers.fasta [2024-01-24 11:35:37,496] [INFO] Task started: Blastn [2024-01-24 11:35:37,497] [INFO] Running command: blastn -query GCF_000959445.1_ASM95944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/reference_markers.fasta -out GCF_000959445.1_ASM95944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:35:38,580] [INFO] Task succeeded: Blastn [2024-01-24 11:35:38,584] [INFO] Selected 13 target genomes. [2024-01-24 11:35:38,584] [INFO] Target genome list was writen to GCF_000959445.1_ASM95944v1_genomic.fna/target_genomes.txt [2024-01-24 11:35:38,600] [INFO] Task started: fastANI [2024-01-24 11:35:38,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg899985fc-6f0d-482e-8501-4dc6ef5fdf27/GCF_000959445.1_ASM95944v1_genomic.fna.gz --refList GCF_000959445.1_ASM95944v1_genomic.fna/target_genomes.txt --output GCF_000959445.1_ASM95944v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:36:05,205] [INFO] Task succeeded: fastANI [2024-01-24 11:36:05,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:36:05,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:36:05,217] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold) [2024-01-24 11:36:05,217] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:36:05,217] [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 vietnamiensis strain=LMG 10929 GCA_000959445.1 60552 60552 type True 100.0 2308 2309 95 conclusive Burkholderia vietnamiensis strain=FDAARGOS_1488 GCA_020099355.1 60552 60552 type True 99.9977 2307 2309 95 conclusive Burkholderia vietnamiensis strain=LMG 10929 GCA_902830295.1 60552 60552 type True 99.9828 2259 2309 95 conclusive Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 90.5432 1631 2309 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 90.4998 1586 2309 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 90.3728 1663 2309 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 90.3158 1633 2309 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.0684 1627 2309 95 below_threshold Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 89.7952 1157 2309 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.0146 1530 2309 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 87.9796 1598 2309 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7293 1332 2309 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.787 1126 2309 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:36:05,219] [INFO] DFAST Taxonomy check result was written to GCF_000959445.1_ASM95944v1_genomic.fna/tc_result.tsv [2024-01-24 11:36:05,220] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:36:05,220] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:36:05,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/checkm_data [2024-01-24 11:36:05,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:36:05,287] [INFO] Task started: CheckM [2024-01-24 11:36:05,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000959445.1_ASM95944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000959445.1_ASM95944v1_genomic.fna/checkm_input GCF_000959445.1_ASM95944v1_genomic.fna/checkm_result [2024-01-24 11:37:17,941] [INFO] Task succeeded: CheckM [2024-01-24 11:37:17,943] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:37:17,967] [INFO] ===== Completeness check finished ===== [2024-01-24 11:37:17,968] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:37:17,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000959445.1_ASM95944v1_genomic.fna/markers.fasta) [2024-01-24 11:37:17,968] [INFO] Task started: Blastn [2024-01-24 11:37:17,969] [INFO] Running command: blastn -query GCF_000959445.1_ASM95944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ebbc4bc-2484-46f1-ab54-e6313aaa9b8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000959445.1_ASM95944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:37:20,050] [INFO] Task succeeded: Blastn [2024-01-24 11:37:20,055] [INFO] Selected 17 target genomes. [2024-01-24 11:37:20,055] [INFO] Target genome list was writen to GCF_000959445.1_ASM95944v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:37:20,063] [INFO] Task started: fastANI [2024-01-24 11:37:20,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg899985fc-6f0d-482e-8501-4dc6ef5fdf27/GCF_000959445.1_ASM95944v1_genomic.fna.gz --refList GCF_000959445.1_ASM95944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000959445.1_ASM95944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:37:53,740] [INFO] Task succeeded: fastANI [2024-01-24 11:37:53,758] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:37:53,758] [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_000959445.1 s__Burkholderia vietnamiensis 100.0 2308 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.93 97.91 0.90 0.83 111 conclusive GCF_000949135.2 s__Burkholderia sp000949135 90.6911 1691 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_003853645.1 s__Burkholderia sp003853645 90.5353 1652 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_003853415.1 s__Burkholderia sp003853415 90.5218 1687 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_902499045.1 s__Burkholderia latens 90.5044 1635 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_000292915.1 s__Burkholderia cepacia_D 90.4759 1518 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003635165.1 s__Burkholderia sp003635165 90.4646 1687 2309 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 90.4147 1716 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.41 95.73 0.89 0.79 83 - GCF_902833055.1 s__Burkholderia territorii 90.3531 1665 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.56 96.71 0.92 0.86 37 - GCF_902499115.1 s__Burkholderia diffusa 90.2698 1682 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 - GCF_001443045.1 s__Burkholderia ambifaria_A 90.2469 1679 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_001718315.1 s__Burkholderia diffusa_B 90.0493 1716 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1139 98.43 98.33 0.91 0.89 12 - GCF_902498995.1 s__Burkholderia anthina 90.034 1617 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.19 0.86 0.77 22 - GCF_902833145.1 s__Burkholderia sp902833145 89.8282 1648 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_016899425.1 s__Burkholderia sp002223185 89.7641 1718 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.86 95.32 0.94 0.84 68 - GCF_001522585.2 s__Burkholderia sp001522585 89.6522 1663 2309 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.44 95.03 0.88 0.83 18 - GCF_001718835.1 s__Burkholderia cepacia_F 88.9494 1600 2309 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 11:37:53,760] [INFO] GTDB search result was written to GCF_000959445.1_ASM95944v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:37:53,761] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:37:53,764] [INFO] DFAST_QC result json was written to GCF_000959445.1_ASM95944v1_genomic.fna/dqc_result.json [2024-01-24 11:37:53,764] [INFO] DFAST_QC completed! [2024-01-24 11:37:53,764] [INFO] Total running time: 0h2m40s