[2024-01-24 13:22:11,381] [INFO] DFAST_QC pipeline started. [2024-01-24 13:22:11,382] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:22:11,383] [INFO] DQC Reference Directory: /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference [2024-01-24 13:22:13,354] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:22:13,355] [INFO] Task started: Prodigal [2024-01-24 13:22:13,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg837089be-a5f5-45c0-ae6f-bf948f7dca44/GCF_005938105.1_ASM593810v1_genomic.fna.gz | prodigal -d GCF_005938105.1_ASM593810v1_genomic.fna/cds.fna -a GCF_005938105.1_ASM593810v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:22:28,087] [INFO] Task succeeded: Prodigal [2024-01-24 13:22:28,088] [INFO] Task started: HMMsearch [2024-01-24 13:22:28,088] [INFO] Running command: hmmsearch --tblout GCF_005938105.1_ASM593810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/reference_markers.hmm GCF_005938105.1_ASM593810v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:22:28,512] [INFO] Task succeeded: HMMsearch [2024-01-24 13:22:28,513] [INFO] Found 6/6 markers. [2024-01-24 13:22:28,562] [INFO] Query marker FASTA was written to GCF_005938105.1_ASM593810v1_genomic.fna/markers.fasta [2024-01-24 13:22:28,562] [INFO] Task started: Blastn [2024-01-24 13:22:28,563] [INFO] Running command: blastn -query GCF_005938105.1_ASM593810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/reference_markers.fasta -out GCF_005938105.1_ASM593810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:22:29,361] [INFO] Task succeeded: Blastn [2024-01-24 13:22:29,363] [INFO] Selected 19 target genomes. [2024-01-24 13:22:29,364] [INFO] Target genome list was writen to GCF_005938105.1_ASM593810v1_genomic.fna/target_genomes.txt [2024-01-24 13:22:29,369] [INFO] Task started: fastANI [2024-01-24 13:22:29,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg837089be-a5f5-45c0-ae6f-bf948f7dca44/GCF_005938105.1_ASM593810v1_genomic.fna.gz --refList GCF_005938105.1_ASM593810v1_genomic.fna/target_genomes.txt --output GCF_005938105.1_ASM593810v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:22:49,635] [INFO] Task succeeded: fastANI [2024-01-24 13:22:49,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:22:49,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:22:49,647] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:22:49,647] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:22:49,648] [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 Brucella haematophila strain=CCUG 38531 GCA_005938105.1 419474 419474 type True 100.0 1808 1810 95 conclusive Brucella tritici strain=LMG 18957 GCA_008932295.1 94626 94626 type True 83.7977 971 1810 95 below_threshold Brucella pecoris strain=DSM 23868 GCA_014197065.1 867683 867683 type True 83.525 977 1810 95 below_threshold Brucella pecoris strain=08RB2639 GCA_006376675.1 867683 867683 type True 83.4983 978 1810 95 below_threshold Brucella anthropi strain=NCTC12168 GCA_900454235.1 529 529 type True 83.1224 994 1810 95 below_threshold Brucella anthropi strain=ATCC 49188 GCA_000017405.1 529 529 type True 83.0569 1013 1810 95 below_threshold Brucella intermedia strain=NCTC12171 GCA_900454225.1 94625 94625 suspected-type True 82.8231 990 1810 95 below_threshold Brucella daejeonensis strain=DSM 26944 GCA_014199265.1 659015 659015 type True 82.4799 894 1810 95 below_threshold Brucella suis strain=NCTC10316 GCA_900460605.1 29461 29461 suspected-type True 82.0516 758 1810 95 below_threshold Brucella suis strain=1330 GCA_000007505.1 29461 29461 suspected-type True 82.0251 766 1810 95 below_threshold Brucella melitensis strain=16M GCA_000250795.2 29459 29459 suspected-type True 81.9825 741 1810 95 below_threshold Brucella ovis strain=ATCC 25840 GCA_000016845.1 236 236 type True 81.9726 761 1810 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_003049685.2 571256 571256 type True 81.3656 829 1810 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_008801705.1 571256 571256 type True 81.3608 825 1810 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 77.953 330 1810 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 77.9352 332 1810 95 below_threshold Mesorhizobium comanense strain=3P27G6 GCA_005503535.1 2502215 2502215 type True 77.3875 300 1810 95 below_threshold Mesorhizobium onobrychidis strain=OM4 GCA_024707545.1 2775404 2775404 type True 77.0381 293 1810 95 below_threshold Nitratireductor alexandrii strain=Z3-1 GCA_004000215.1 2448161 2448161 type True 76.9179 250 1810 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:22:49,649] [INFO] DFAST Taxonomy check result was written to GCF_005938105.1_ASM593810v1_genomic.fna/tc_result.tsv [2024-01-24 13:22:49,649] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:22:49,650] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:22:49,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/checkm_data [2024-01-24 13:22:49,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:22:49,702] [INFO] Task started: CheckM [2024-01-24 13:22:49,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938105.1_ASM593810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938105.1_ASM593810v1_genomic.fna/checkm_input GCF_005938105.1_ASM593810v1_genomic.fna/checkm_result [2024-01-24 13:23:32,585] [INFO] Task succeeded: CheckM [2024-01-24 13:23:32,586] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:23:32,600] [INFO] ===== Completeness check finished ===== [2024-01-24 13:23:32,600] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:23:32,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938105.1_ASM593810v1_genomic.fna/markers.fasta) [2024-01-24 13:23:32,600] [INFO] Task started: Blastn [2024-01-24 13:23:32,600] [INFO] Running command: blastn -query GCF_005938105.1_ASM593810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e6d374-88d1-4a86-8cca-b9753ae3fa5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938105.1_ASM593810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:23:34,035] [INFO] Task succeeded: Blastn [2024-01-24 13:23:34,037] [INFO] Selected 5 target genomes. [2024-01-24 13:23:34,038] [INFO] Target genome list was writen to GCF_005938105.1_ASM593810v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:23:34,041] [INFO] Task started: fastANI [2024-01-24 13:23:34,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg837089be-a5f5-45c0-ae6f-bf948f7dca44/GCF_005938105.1_ASM593810v1_genomic.fna.gz --refList GCF_005938105.1_ASM593810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938105.1_ASM593810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:23:41,289] [INFO] Task succeeded: fastANI [2024-01-24 13:23:41,293] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:23:41,293] [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_005938105.1 s__Ochrobactrum_B haematophila 100.0 1808 1810 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B 95.0 98.61 97.38 0.92 0.84 3 conclusive GCA_900465685.1 s__Ochrobactrum_B sp900465685 94.7719 1462 1810 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B 95.0 99.22 99.21 0.91 0.91 3 - GCF_014138095.1 s__Ochrobactrum_B sp014138095 92.6804 1403 1810 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B 95.0 N/A N/A N/A N/A 1 - GCF_016427605.1 s__Ochrobactrum_B sp016427605 91.184 1307 1810 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B 95.0 N/A N/A N/A N/A 1 - GCF_006376685.1 s__Ochrobactrum_B teleogrylli 89.9505 1310 1810 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B 95.0 98.13 98.09 0.91 0.90 5 - -------------------------------------------------------------------------------- [2024-01-24 13:23:41,295] [INFO] GTDB search result was written to GCF_005938105.1_ASM593810v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:23:41,295] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:23:41,298] [INFO] DFAST_QC result json was written to GCF_005938105.1_ASM593810v1_genomic.fna/dqc_result.json [2024-01-24 13:23:41,298] [INFO] DFAST_QC completed! [2024-01-24 13:23:41,298] [INFO] Total running time: 0h1m30s