[2024-01-24 12:44:52,217] [INFO] DFAST_QC pipeline started. [2024-01-24 12:44:52,219] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:44:52,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference [2024-01-24 12:44:53,451] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:44:53,452] [INFO] Task started: Prodigal [2024-01-24 12:44:53,452] [INFO] Running command: gunzip -c /var/lib/cwl/stge594ac77-9a57-4529-84e3-9a70bb55d282/GCF_902830295.1_ASM90283029v1_genomic.fna.gz | prodigal -d GCF_902830295.1_ASM90283029v1_genomic.fna/cds.fna -a GCF_902830295.1_ASM90283029v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:45:14,222] [INFO] Task succeeded: Prodigal [2024-01-24 12:45:14,223] [INFO] Task started: HMMsearch [2024-01-24 12:45:14,223] [INFO] Running command: hmmsearch --tblout GCF_902830295.1_ASM90283029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/reference_markers.hmm GCF_902830295.1_ASM90283029v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:45:14,549] [INFO] Task succeeded: HMMsearch [2024-01-24 12:45:14,551] [INFO] Found 6/6 markers. [2024-01-24 12:45:14,607] [INFO] Query marker FASTA was written to GCF_902830295.1_ASM90283029v1_genomic.fna/markers.fasta [2024-01-24 12:45:14,607] [INFO] Task started: Blastn [2024-01-24 12:45:14,607] [INFO] Running command: blastn -query GCF_902830295.1_ASM90283029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/reference_markers.fasta -out GCF_902830295.1_ASM90283029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:45:15,681] [INFO] Task succeeded: Blastn [2024-01-24 12:45:15,686] [INFO] Selected 13 target genomes. [2024-01-24 12:45:15,687] [INFO] Target genome list was writen to GCF_902830295.1_ASM90283029v1_genomic.fna/target_genomes.txt [2024-01-24 12:45:15,706] [INFO] Task started: fastANI [2024-01-24 12:45:15,706] [INFO] Running command: fastANI --query /var/lib/cwl/stge594ac77-9a57-4529-84e3-9a70bb55d282/GCF_902830295.1_ASM90283029v1_genomic.fna.gz --refList GCF_902830295.1_ASM90283029v1_genomic.fna/target_genomes.txt --output GCF_902830295.1_ASM90283029v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:45:40,901] [INFO] Task succeeded: fastANI [2024-01-24 12:45:40,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:45:40,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:45:40,919] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold) [2024-01-24 12:45:40,919] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:45:40,919] [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_902830295.1 60552 60552 type True 100.0 2268 2270 95 conclusive Burkholderia vietnamiensis strain=FDAARGOS_1488 GCA_020099355.1 60552 60552 type True 99.9949 2266 2270 95 conclusive Burkholderia vietnamiensis strain=LMG 10929 GCA_000959445.1 60552 60552 type True 99.993 2267 2270 95 conclusive Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 90.5887 1627 2270 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 90.5062 1566 2270 95 below_threshold Burkholderia territorii strain=LMG 28158 GCA_902833055.1 1503055 1503055 type True 90.3364 1654 2270 95 below_threshold Burkholderia territorii GCA_902499035.1 1503055 1503055 type True 90.3076 1623 2270 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 90.0343 1621 2270 95 below_threshold Burkholderia territorii strain=CCUG 65687 GCA_008802115.1 1503055 1503055 type True 89.8839 1147 2270 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.0701 1572 2270 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 87.9584 1541 2270 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.7252 1333 2270 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.8546 1110 2270 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:45:40,921] [INFO] DFAST Taxonomy check result was written to GCF_902830295.1_ASM90283029v1_genomic.fna/tc_result.tsv [2024-01-24 12:45:40,922] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:45:40,923] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:45:40,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/checkm_data [2024-01-24 12:45:40,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:45:40,989] [INFO] Task started: CheckM [2024-01-24 12:45:40,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902830295.1_ASM90283029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902830295.1_ASM90283029v1_genomic.fna/checkm_input GCF_902830295.1_ASM90283029v1_genomic.fna/checkm_result [2024-01-24 12:46:48,567] [INFO] Task succeeded: CheckM [2024-01-24 12:46:48,569] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:46:48,590] [INFO] ===== Completeness check finished ===== [2024-01-24 12:46:48,590] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:46:48,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902830295.1_ASM90283029v1_genomic.fna/markers.fasta) [2024-01-24 12:46:48,591] [INFO] Task started: Blastn [2024-01-24 12:46:48,591] [INFO] Running command: blastn -query GCF_902830295.1_ASM90283029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2453b3-cf4c-42cd-b167-0ffdf7829fa0/dqc_reference/reference_markers_gtdb.fasta -out GCF_902830295.1_ASM90283029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:46:50,669] [INFO] Task succeeded: Blastn [2024-01-24 12:46:50,675] [INFO] Selected 16 target genomes. [2024-01-24 12:46:50,675] [INFO] Target genome list was writen to GCF_902830295.1_ASM90283029v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:46:50,689] [INFO] Task started: fastANI [2024-01-24 12:46:50,690] [INFO] Running command: fastANI --query /var/lib/cwl/stge594ac77-9a57-4529-84e3-9a70bb55d282/GCF_902830295.1_ASM90283029v1_genomic.fna.gz --refList GCF_902830295.1_ASM90283029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902830295.1_ASM90283029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:47:22,307] [INFO] Task succeeded: fastANI [2024-01-24 12:47:22,332] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:47:22,333] [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 99.993 2267 2270 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_003853415.1 s__Burkholderia sp003853415 90.6151 1678 2270 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.32 99.32 0.91 0.91 2 - GCF_000949135.2 s__Burkholderia sp000949135 90.5982 1695 2270 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 90.5729 1647 2270 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.08 96.08 0.79 0.79 2 - GCF_902499045.1 s__Burkholderia latens 90.5612 1631 2270 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 90.4051 1527 2270 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 90.4033 1683 2270 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 90.4022 1716 2270 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 90.3487 1653 2270 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 90.3223 1662 2270 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 90.2359 1665 2270 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 90.0686 1695 2270 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 89.975 1623 2270 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 89.7713 1642 2270 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_001522585.2 s__Burkholderia sp001522585 89.6242 1656 2270 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 88.9531 1604 2270 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 12:47:22,334] [INFO] GTDB search result was written to GCF_902830295.1_ASM90283029v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:47:22,335] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:47:22,340] [INFO] DFAST_QC result json was written to GCF_902830295.1_ASM90283029v1_genomic.fna/dqc_result.json [2024-01-24 12:47:22,340] [INFO] DFAST_QC completed! [2024-01-24 12:47:22,340] [INFO] Total running time: 0h2m30s