[2024-01-25 18:14:50,549] [INFO] DFAST_QC pipeline started. [2024-01-25 18:14:50,552] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:14:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference [2024-01-25 18:14:51,667] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:14:51,667] [INFO] Task started: Prodigal [2024-01-25 18:14:51,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg63c751f7-6f52-46fa-898a-c42be8ad06d4/GCF_003628145.1_ASM362814v1_genomic.fna.gz | prodigal -d GCF_003628145.1_ASM362814v1_genomic.fna/cds.fna -a GCF_003628145.1_ASM362814v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:15:12,381] [INFO] Task succeeded: Prodigal [2024-01-25 18:15:12,381] [INFO] Task started: HMMsearch [2024-01-25 18:15:12,381] [INFO] Running command: hmmsearch --tblout GCF_003628145.1_ASM362814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/reference_markers.hmm GCF_003628145.1_ASM362814v1_genomic.fna/protein.faa > /dev/null [2024-01-25 18:15:12,634] [INFO] Task succeeded: HMMsearch [2024-01-25 18:15:12,635] [INFO] Found 6/6 markers. [2024-01-25 18:15:12,680] [INFO] Query marker FASTA was written to GCF_003628145.1_ASM362814v1_genomic.fna/markers.fasta [2024-01-25 18:15:12,681] [INFO] Task started: Blastn [2024-01-25 18:15:12,681] [INFO] Running command: blastn -query GCF_003628145.1_ASM362814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/reference_markers.fasta -out GCF_003628145.1_ASM362814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:15:13,651] [INFO] Task succeeded: Blastn [2024-01-25 18:15:13,654] [INFO] Selected 27 target genomes. [2024-01-25 18:15:13,654] [INFO] Target genome list was writen to GCF_003628145.1_ASM362814v1_genomic.fna/target_genomes.txt [2024-01-25 18:15:13,668] [INFO] Task started: fastANI [2024-01-25 18:15:13,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c751f7-6f52-46fa-898a-c42be8ad06d4/GCF_003628145.1_ASM362814v1_genomic.fna.gz --refList GCF_003628145.1_ASM362814v1_genomic.fna/target_genomes.txt --output GCF_003628145.1_ASM362814v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:15:47,056] [INFO] Task succeeded: fastANI [2024-01-25 18:15:47,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:15:47,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:15:47,072] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold) [2024-01-25 18:15:47,072] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-25 18:15:47,072] [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 Trinickia dinghuensis strain=DHOM06 GCA_003367175.1 2291023 2291023 type True 82.1206 963 2017 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000286555.1 87883 87883 type True 81.8695 747 2017 95 below_threshold Burkholderia multivorans strain=NCTC13007 GCA_900446205.1 87883 87883 type True 81.8597 859 2017 95 below_threshold Burkholderia multivorans strain=ATCC BAA-247 GCA_000959525.1 87883 87883 type True 81.7938 863 2017 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 81.6155 916 2017 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 81.612 961 2017 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 81.5932 858 2017 95 below_threshold Burkholderia oklahomensis strain=LMG 23618 GCA_900608545.1 342113 342113 type True 81.5475 924 2017 95 below_threshold Burkholderia pseudomallei strain=WRAIR 286 GCA_006538545.1 28450 28450 type True 81.5026 904 2017 95 below_threshold Burkholderia thailandensis strain=E264; ATCC 700388 GCA_000012365.1 57975 57975 type True 81.4979 904 2017 95 below_threshold Burkholderia thailandensis strain=E264 GCA_003568605.1 57975 57975 type True 81.4756 897 2017 95 below_threshold Burkholderia mallei strain=ATCC 23344 GCA_000011705.1 13373 13373 type True 81.468 854 2017 95 below_threshold Burkholderia mayonis strain=BDU6 GCA_001523745.2 1385591 1385591 type True 81.4426 880 2017 95 below_threshold Trinickia soli strain=LMG 24076 GCA_902859815.1 380675 380675 type True 81.4055 920 2017 95 below_threshold Burkholderia pseudomallei strain=ATCC 23343 GCA_001182285.1 28450 28450 type True 81.4016 934 2017 95 below_threshold Trinickia soli strain=GP25-8 GCA_002879855.1 380675 380675 type True 81.3977 914 2017 95 below_threshold Burkholderia thailandensis strain=ATCC 700388 GCA_000152285.1 57975 57975 type True 81.3969 844 2017 95 below_threshold Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 81.3433 860 2017 95 below_threshold Trinickia diaoshuihuensis strain=NEAU-SY24 GCA_003390925.1 2292265 2292265 type True 81.3291 896 2017 95 below_threshold Paraburkholderia caballeronis strain=TNe-841 GCA_900104845.1 416943 416943 type True 81.3083 876 2017 95 below_threshold Trinickia dabaoshanensis strain=GIMN1.004 GCA_002879885.1 564714 564714 type True 81.3073 954 2017 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 81.3043 842 2017 95 below_threshold Paraburkholderia caballeronis strain=LMG 26416 GCA_900109675.1 416943 416943 type True 81.2715 859 2017 95 below_threshold Burkholderia anthina strain=DSM 16086 GCA_016836725.1 179879 179879 suspected-type True 81.1876 885 2017 95 below_threshold Trinickia symbiotica strain=JPY-345 GCA_002934455.1 863227 863227 type True 81.1833 839 2017 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.7914 916 2017 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 80.7101 744 2017 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:15:47,082] [INFO] DFAST Taxonomy check result was written to GCF_003628145.1_ASM362814v1_genomic.fna/tc_result.tsv [2024-01-25 18:15:47,082] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:15:47,082] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:15:47,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/checkm_data [2024-01-25 18:15:47,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:15:47,139] [INFO] Task started: CheckM [2024-01-25 18:15:47,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628145.1_ASM362814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628145.1_ASM362814v1_genomic.fna/checkm_input GCF_003628145.1_ASM362814v1_genomic.fna/checkm_result [2024-01-25 18:16:49,759] [INFO] Task succeeded: CheckM [2024-01-25 18:16:49,760] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:16:49,782] [INFO] ===== Completeness check finished ===== [2024-01-25 18:16:49,782] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:16:49,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628145.1_ASM362814v1_genomic.fna/markers.fasta) [2024-01-25 18:16:49,783] [INFO] Task started: Blastn [2024-01-25 18:16:49,783] [INFO] Running command: blastn -query GCF_003628145.1_ASM362814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4443888a-6dfe-453d-b77a-4ba264ef7f11/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628145.1_ASM362814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:16:51,860] [INFO] Task succeeded: Blastn [2024-01-25 18:16:51,863] [INFO] Selected 22 target genomes. [2024-01-25 18:16:51,863] [INFO] Target genome list was writen to GCF_003628145.1_ASM362814v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:16:51,914] [INFO] Task started: fastANI [2024-01-25 18:16:51,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c751f7-6f52-46fa-898a-c42be8ad06d4/GCF_003628145.1_ASM362814v1_genomic.fna.gz --refList GCF_003628145.1_ASM362814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628145.1_ASM362814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:17:21,508] [INFO] Task succeeded: fastANI [2024-01-25 18:17:21,521] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:17:21,521] [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_003628145.1 s__Trinickia fusca 100.0 2016 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 conclusive GCF_017315705.1 s__Trinickia sp017315705 82.2312 914 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_005280735.1 s__Trinickia sp005280735 82.1762 1009 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_003367175.1 s__Trinickia dinghuensis 82.1286 962 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_005144415.1 s__Trinickia sp005144415 82.1128 968 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_017315725.1 s__Trinickia sp017315725 82.0622 955 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_000959525.1 s__Burkholderia multivorans 81.7878 864 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.58 96.90 0.90 0.85 326 - GCF_000687455.2 s__Burkholderia sp000687455 81.6971 761 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499075.1 s__Burkholderia pseudomultivorans 81.5657 861 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_001524625.2 s__Burkholderia sp001524625 81.564 926 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.38 99.33 0.93 0.91 11 - GCF_000959365.1 s__Burkholderia oklahomensis 81.486 933 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.42 95.09 0.95 0.85 15 - GCF_000012365.1 s__Burkholderia thailandensis 81.4598 909 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.58 98.83 0.96 0.93 53 - GCF_000011705.1 s__Burkholderia mallei 81.417 860 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.31 98.71 0.94 0.78 1780 - GCF_002879855.1 s__Trinickia soli 81.398 914 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 99.68 99.37 0.95 0.90 3 - GCF_902499045.1 s__Burkholderia latens 81.3876 854 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_003854275.1 s__Burkholderia sp003854275 81.3506 904 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_001718795.1 s__Burkholderia latens_A 81.3307 816 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.33 99.18 0.94 0.92 8 - GCF_003390925.1 s__Trinickia diaoshuihuensis 81.3262 896 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_002879885.1 s__Trinickia dabaoshanensis 81.3005 955 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_900104845.1 s__Paraburkholderia caballeronis 81.283 880 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.48 98.95 0.97 0.92 9 - GCA_004322045.1 s__Trinickia sp004322045 81.1635 833 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 96.62 96.62 0.93 0.93 2 - GCF_002934455.1 s__Trinickia symbiotica 81.1592 842 2017 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 98.34 95.03 0.94 0.86 4 - -------------------------------------------------------------------------------- [2024-01-25 18:17:21,522] [INFO] GTDB search result was written to GCF_003628145.1_ASM362814v1_genomic.fna/result_gtdb.tsv [2024-01-25 18:17:21,523] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:17:21,527] [INFO] DFAST_QC result json was written to GCF_003628145.1_ASM362814v1_genomic.fna/dqc_result.json [2024-01-25 18:17:21,527] [INFO] DFAST_QC completed! [2024-01-25 18:17:21,527] [INFO] Total running time: 0h2m31s