[2024-01-25 19:11:35,675] [INFO] DFAST_QC pipeline started. [2024-01-25 19:11:35,678] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:11:35,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference [2024-01-25 19:11:36,851] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:11:36,851] [INFO] Task started: Prodigal [2024-01-25 19:11:36,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg02a0edb1-ca11-4aab-a791-0533a0684d98/GCF_002252475.1_ASM225247v1_genomic.fna.gz | prodigal -d GCF_002252475.1_ASM225247v1_genomic.fna/cds.fna -a GCF_002252475.1_ASM225247v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:11:49,835] [INFO] Task succeeded: Prodigal [2024-01-25 19:11:49,835] [INFO] Task started: HMMsearch [2024-01-25 19:11:49,835] [INFO] Running command: hmmsearch --tblout GCF_002252475.1_ASM225247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/reference_markers.hmm GCF_002252475.1_ASM225247v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:11:50,155] [INFO] Task succeeded: HMMsearch [2024-01-25 19:11:50,156] [INFO] Found 6/6 markers. [2024-01-25 19:11:50,203] [INFO] Query marker FASTA was written to GCF_002252475.1_ASM225247v1_genomic.fna/markers.fasta [2024-01-25 19:11:50,203] [INFO] Task started: Blastn [2024-01-25 19:11:50,203] [INFO] Running command: blastn -query GCF_002252475.1_ASM225247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/reference_markers.fasta -out GCF_002252475.1_ASM225247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:11:50,850] [INFO] Task succeeded: Blastn [2024-01-25 19:11:50,853] [INFO] Selected 13 target genomes. [2024-01-25 19:11:50,853] [INFO] Target genome list was writen to GCF_002252475.1_ASM225247v1_genomic.fna/target_genomes.txt [2024-01-25 19:11:50,863] [INFO] Task started: fastANI [2024-01-25 19:11:50,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a0edb1-ca11-4aab-a791-0533a0684d98/GCF_002252475.1_ASM225247v1_genomic.fna.gz --refList GCF_002252475.1_ASM225247v1_genomic.fna/target_genomes.txt --output GCF_002252475.1_ASM225247v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:12:02,884] [INFO] Task succeeded: fastANI [2024-01-25 19:12:02,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:12:02,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:12:02,893] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold) [2024-01-25 19:12:02,893] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:12:02,893] [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 rhizosphaerae strain=PR17 GCA_002252475.1 571254 571254 type True 100.0 1615 1616 95 conclusive [Ochrobactrum] quorumnocens strain=A44 GCA_002278035.1 271865 271865 type True 88.1163 1295 1616 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_008801705.1 571256 571256 type True 87.339 1255 1616 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_003049685.2 571256 571256 type True 87.2652 1289 1616 95 below_threshold Brucella grignonensis strain=OgA9a GCA_002252505.1 94627 94627 type True 86.3611 1139 1616 95 below_threshold Brucella intermedia strain=NCTC12171 GCA_900454225.1 94625 94625 suspected-type True 80.0234 742 1616 95 below_threshold Brucella intermedia strain=LMG 3301 GCA_000182645.1 94625 94625 suspected-type True 79.909 765 1616 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 77.8694 256 1616 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 77.8151 255 1616 95 below_threshold Pseudochrobactrum asaccharolyticum strain=DSM 25619 GCA_003314995.1 354351 354351 type True 77.7197 245 1616 95 below_threshold Rhizobium skierniewicense strain=Ch11 GCA_023757665.1 984260 984260 type True 76.8197 126 1616 95 below_threshold Pseudaminobacter soli strain=HC19 GCA_014595955.1 2831468 2831468 type True 76.1658 99 1616 95 below_threshold Pseudaminobacter soli strain=19-2017 GCA_018310375.1 2831468 2831468 type True 76.1658 99 1616 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:12:02,895] [INFO] DFAST Taxonomy check result was written to GCF_002252475.1_ASM225247v1_genomic.fna/tc_result.tsv [2024-01-25 19:12:02,895] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:12:02,895] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:12:02,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/checkm_data [2024-01-25 19:12:02,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:12:02,944] [INFO] Task started: CheckM [2024-01-25 19:12:02,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002252475.1_ASM225247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002252475.1_ASM225247v1_genomic.fna/checkm_input GCF_002252475.1_ASM225247v1_genomic.fna/checkm_result [2024-01-25 19:12:42,275] [INFO] Task succeeded: CheckM [2024-01-25 19:12:42,276] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:12:42,295] [INFO] ===== Completeness check finished ===== [2024-01-25 19:12:42,295] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:12:42,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002252475.1_ASM225247v1_genomic.fna/markers.fasta) [2024-01-25 19:12:42,295] [INFO] Task started: Blastn [2024-01-25 19:12:42,295] [INFO] Running command: blastn -query GCF_002252475.1_ASM225247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a4d65e-4232-474b-9316-762916ed1c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002252475.1_ASM225247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:12:43,277] [INFO] Task succeeded: Blastn [2024-01-25 19:12:43,281] [INFO] Selected 9 target genomes. [2024-01-25 19:12:43,281] [INFO] Target genome list was writen to GCF_002252475.1_ASM225247v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:12:43,294] [INFO] Task started: fastANI [2024-01-25 19:12:43,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a0edb1-ca11-4aab-a791-0533a0684d98/GCF_002252475.1_ASM225247v1_genomic.fna.gz --refList GCF_002252475.1_ASM225247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002252475.1_ASM225247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:12:53,287] [INFO] Task succeeded: fastANI [2024-01-25 19:12:53,294] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:12:53,295] [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_002252475.1 s__Ochrobactrum_A rhizosphaerae 100.0 1615 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 N/A N/A N/A N/A 1 conclusive GCF_002278035.1 s__Ochrobactrum_A quorumnocens 88.106 1296 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 97.19 96.78 0.85 0.82 5 - GCF_003049685.1 s__Ochrobactrum_A pituitosa 87.2786 1287 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 98.27 97.05 0.91 0.82 14 - GCF_004368705.1 s__Ochrobactrum_A sp004368705 86.499 1283 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 N/A N/A N/A N/A 1 - GCF_002252505.1 s__Ochrobactrum_A grignonensis 86.3683 1139 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 99.78 99.78 1.00 1.00 2 - GCF_002252445.1 s__Ochrobactrum_A thiophenivorans 82.6557 910 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 N/A N/A N/A N/A 1 - GCF_000182645.1 s__Ochrobactrum intermedium 79.909 765 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum 95.0 97.99 97.16 0.92 0.84 56 - GCF_003314995.1 s__Pseudochrobactrum asaccharolyticum 77.7322 244 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum 95.0 95.18 95.14 0.85 0.85 3 - GCF_013327855.1 s__Phyllobacterium pellucidum 77.1585 179 1616 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium 95.0 97.81 96.22 0.94 0.90 6 - -------------------------------------------------------------------------------- [2024-01-25 19:12:53,296] [INFO] GTDB search result was written to GCF_002252475.1_ASM225247v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:12:53,297] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:12:53,299] [INFO] DFAST_QC result json was written to GCF_002252475.1_ASM225247v1_genomic.fna/dqc_result.json [2024-01-25 19:12:53,300] [INFO] DFAST_QC completed! [2024-01-25 19:12:53,300] [INFO] Total running time: 0h1m18s