[2024-01-24 13:46:18,308] [INFO] DFAST_QC pipeline started. [2024-01-24 13:46:18,309] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:46:18,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference [2024-01-24 13:46:19,675] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:46:19,676] [INFO] Task started: Prodigal [2024-01-24 13:46:19,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8370c77-c460-4e1f-a0ab-c98c2767a2b2/GCF_902830395.1_ASM90283039v1_genomic.fna.gz | prodigal -d GCF_902830395.1_ASM90283039v1_genomic.fna/cds.fna -a GCF_902830395.1_ASM90283039v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:46:42,862] [INFO] Task succeeded: Prodigal [2024-01-24 13:46:42,862] [INFO] Task started: HMMsearch [2024-01-24 13:46:42,862] [INFO] Running command: hmmsearch --tblout GCF_902830395.1_ASM90283039v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/reference_markers.hmm GCF_902830395.1_ASM90283039v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:46:43,303] [INFO] Task succeeded: HMMsearch [2024-01-24 13:46:43,304] [INFO] Found 6/6 markers. [2024-01-24 13:46:43,367] [INFO] Query marker FASTA was written to GCF_902830395.1_ASM90283039v1_genomic.fna/markers.fasta [2024-01-24 13:46:43,368] [INFO] Task started: Blastn [2024-01-24 13:46:43,368] [INFO] Running command: blastn -query GCF_902830395.1_ASM90283039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/reference_markers.fasta -out GCF_902830395.1_ASM90283039v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:46:44,488] [INFO] Task succeeded: Blastn [2024-01-24 13:46:44,491] [INFO] Selected 15 target genomes. [2024-01-24 13:46:44,491] [INFO] Target genome list was writen to GCF_902830395.1_ASM90283039v1_genomic.fna/target_genomes.txt [2024-01-24 13:46:44,495] [INFO] Task started: fastANI [2024-01-24 13:46:44,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8370c77-c460-4e1f-a0ab-c98c2767a2b2/GCF_902830395.1_ASM90283039v1_genomic.fna.gz --refList GCF_902830395.1_ASM90283039v1_genomic.fna/target_genomes.txt --output GCF_902830395.1_ASM90283039v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:47:18,107] [INFO] Task succeeded: fastANI [2024-01-24 13:47:18,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:47:18,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:47:18,125] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold) [2024-01-24 13:47:18,125] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:47:18,125] [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 anthina strain=LMG 20980 GCA_902830395.1 179879 179879 suspected-type True 100.0 2515 2518 95 conclusive Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 99.9919 2487 2518 95 conclusive Burkholderia anthina GCA_902498995.1 179879 179879 suspected-type True 99.9901 2485 2518 95 conclusive Burkholderia diffusa GCA_902499115.1 488732 488732 suspected-type True 92.0247 1790 2518 95 below_threshold Burkholderia diffusa strain=DSM 23434 GCA_016836765.1 488732 488732 suspected-type True 92.0061 1797 2518 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000959545.1 152480 152480 type True 91.9501 1823 2518 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 91.9348 1829 2518 95 below_threshold Burkholderia cenocepacia strain=NCTC13227 GCA_900446215.1 95486 95486 type True 90.9398 1866 2518 95 below_threshold Burkholderia seminalis strain=LMG 24067 GCA_902832885.1 488731 488731 type True 90.8145 1851 2518 95 below_threshold Burkholderia seminalis GCA_902499165.1 488731 488731 type True 90.7669 1809 2518 95 below_threshold Burkholderia lata strain=383 GCA_000012945.1 482957 482957 suspected-type True 90.6426 1935 2518 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 88.4372 1663 2518 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 88.4183 1705 2518 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 83.6012 1366 2518 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 81.1989 1228 2518 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:47:18,127] [INFO] DFAST Taxonomy check result was written to GCF_902830395.1_ASM90283039v1_genomic.fna/tc_result.tsv [2024-01-24 13:47:18,127] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:47:18,127] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:47:18,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/checkm_data [2024-01-24 13:47:18,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:47:18,198] [INFO] Task started: CheckM [2024-01-24 13:47:18,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902830395.1_ASM90283039v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902830395.1_ASM90283039v1_genomic.fna/checkm_input GCF_902830395.1_ASM90283039v1_genomic.fna/checkm_result [2024-01-24 13:48:32,711] [INFO] Task succeeded: CheckM [2024-01-24 13:48:32,712] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:48:32,736] [INFO] ===== Completeness check finished ===== [2024-01-24 13:48:32,736] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:48:32,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902830395.1_ASM90283039v1_genomic.fna/markers.fasta) [2024-01-24 13:48:32,737] [INFO] Task started: Blastn [2024-01-24 13:48:32,737] [INFO] Running command: blastn -query GCF_902830395.1_ASM90283039v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221bf351-cd22-4449-9565-eb431544b363/dqc_reference/reference_markers_gtdb.fasta -out GCF_902830395.1_ASM90283039v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:48:34,865] [INFO] Task succeeded: Blastn [2024-01-24 13:48:34,869] [INFO] Selected 11 target genomes. [2024-01-24 13:48:34,870] [INFO] Target genome list was writen to GCF_902830395.1_ASM90283039v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:48:34,883] [INFO] Task started: fastANI [2024-01-24 13:48:34,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8370c77-c460-4e1f-a0ab-c98c2767a2b2/GCF_902830395.1_ASM90283039v1_genomic.fna.gz --refList GCF_902830395.1_ASM90283039v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902830395.1_ASM90283039v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:48:59,378] [INFO] Task succeeded: fastANI [2024-01-24 13:48:59,391] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:48:59,391] [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_902498995.1 s__Burkholderia anthina 99.9901 2485 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.19 0.86 0.77 22 conclusive GCF_003853415.1 s__Burkholderia sp003853415 92.4732 1838 2518 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 92.4222 1838 2518 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 92.4222 1781 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000949135.2 s__Burkholderia sp000949135 92.3479 1891 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.23 98.18 0.87 0.85 15 - GCF_001443045.1 s__Burkholderia ambifaria_A 92.2634 1883 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.26 99.26 0.91 0.91 2 - GCF_902499115.1 s__Burkholderia diffusa 91.9809 1795 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.35 95.51 0.88 0.82 18 - GCF_000203915.1 s__Burkholderia ambifaria 91.9413 1828 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.41 95.73 0.89 0.79 83 - GCF_003635165.1 s__Burkholderia sp003635165 91.848 1813 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900446215.1 s__Burkholderia cenocepacia 90.9766 1862 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.1666 99.08 98.68 0.89 0.81 292 - GCF_902833145.1 s__Burkholderia sp902833145 90.7691 1774 2518 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - -------------------------------------------------------------------------------- [2024-01-24 13:48:59,397] [INFO] GTDB search result was written to GCF_902830395.1_ASM90283039v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:48:59,398] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:48:59,403] [INFO] DFAST_QC result json was written to GCF_902830395.1_ASM90283039v1_genomic.fna/dqc_result.json [2024-01-24 13:48:59,403] [INFO] DFAST_QC completed! [2024-01-24 13:48:59,403] [INFO] Total running time: 0h2m41s