[2024-01-24 14:39:29,296] [INFO] DFAST_QC pipeline started. [2024-01-24 14:39:29,298] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:39:29,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference [2024-01-24 14:39:30,571] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:39:30,572] [INFO] Task started: Prodigal [2024-01-24 14:39:30,572] [INFO] Running command: gunzip -c /var/lib/cwl/stgf75b3c2f-03be-41ea-915b-424c47d998b1/GCF_030362795.1_ASM3036279v1_genomic.fna.gz | prodigal -d GCF_030362795.1_ASM3036279v1_genomic.fna/cds.fna -a GCF_030362795.1_ASM3036279v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:39:43,434] [INFO] Task succeeded: Prodigal [2024-01-24 14:39:43,434] [INFO] Task started: HMMsearch [2024-01-24 14:39:43,434] [INFO] Running command: hmmsearch --tblout GCF_030362795.1_ASM3036279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/reference_markers.hmm GCF_030362795.1_ASM3036279v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:39:43,692] [INFO] Task succeeded: HMMsearch [2024-01-24 14:39:43,693] [INFO] Found 6/6 markers. [2024-01-24 14:39:43,738] [INFO] Query marker FASTA was written to GCF_030362795.1_ASM3036279v1_genomic.fna/markers.fasta [2024-01-24 14:39:43,738] [INFO] Task started: Blastn [2024-01-24 14:39:43,738] [INFO] Running command: blastn -query GCF_030362795.1_ASM3036279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/reference_markers.fasta -out GCF_030362795.1_ASM3036279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:39:44,530] [INFO] Task succeeded: Blastn [2024-01-24 14:39:44,533] [INFO] Selected 8 target genomes. [2024-01-24 14:39:44,533] [INFO] Target genome list was writen to GCF_030362795.1_ASM3036279v1_genomic.fna/target_genomes.txt [2024-01-24 14:39:44,537] [INFO] Task started: fastANI [2024-01-24 14:39:44,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75b3c2f-03be-41ea-915b-424c47d998b1/GCF_030362795.1_ASM3036279v1_genomic.fna.gz --refList GCF_030362795.1_ASM3036279v1_genomic.fna/target_genomes.txt --output GCF_030362795.1_ASM3036279v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:39:52,391] [INFO] Task succeeded: fastANI [2024-01-24 14:39:52,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:39:52,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:39:52,400] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold) [2024-01-24 14:39:52,400] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 14:39:52,400] [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 Pseudochrobactrum asaccharolyticum strain=DSM 25619 GCA_003314995.1 354351 354351 type True 90.1933 1179 1468 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 86.2374 1047 1468 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 86.2265 1048 1468 95 below_threshold Pseudochrobactrum saccharolyticum strain=DSM 25620 GCA_014203195.1 354352 354352 type True 86.208 991 1468 95 below_threshold Pseudochrobactrum saccharolyticum strain=CCUG 33852 GCA_008801715.1 354352 354352 type True 86.1835 1001 1468 95 below_threshold Rhizobium skierniewicense strain=Ch11 GCA_023757665.1 984260 984260 type True 76.4381 88 1468 95 below_threshold Agrobacterium salinitolerans strain=YIC 5082 GCA_002008225.1 1183413 1183413 type True 76.4047 110 1468 95 below_threshold Agrobacterium leguminum strain=MOPV5 GCA_015704895.1 2792015 2792015 type True 76.3117 105 1468 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:39:52,402] [INFO] DFAST Taxonomy check result was written to GCF_030362795.1_ASM3036279v1_genomic.fna/tc_result.tsv [2024-01-24 14:39:52,403] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:39:52,403] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:39:52,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/checkm_data [2024-01-24 14:39:52,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:39:52,451] [INFO] Task started: CheckM [2024-01-24 14:39:52,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030362795.1_ASM3036279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030362795.1_ASM3036279v1_genomic.fna/checkm_input GCF_030362795.1_ASM3036279v1_genomic.fna/checkm_result [2024-01-24 14:40:32,334] [INFO] Task succeeded: CheckM [2024-01-24 14:40:32,335] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:40:32,354] [INFO] ===== Completeness check finished ===== [2024-01-24 14:40:32,354] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:40:32,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030362795.1_ASM3036279v1_genomic.fna/markers.fasta) [2024-01-24 14:40:32,355] [INFO] Task started: Blastn [2024-01-24 14:40:32,355] [INFO] Running command: blastn -query GCF_030362795.1_ASM3036279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33627c27-3dba-4bc0-8d70-a7916db1623a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030362795.1_ASM3036279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:40:33,613] [INFO] Task succeeded: Blastn [2024-01-24 14:40:33,617] [INFO] Selected 16 target genomes. [2024-01-24 14:40:33,617] [INFO] Target genome list was writen to GCF_030362795.1_ASM3036279v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:40:33,628] [INFO] Task started: fastANI [2024-01-24 14:40:33,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75b3c2f-03be-41ea-915b-424c47d998b1/GCF_030362795.1_ASM3036279v1_genomic.fna.gz --refList GCF_030362795.1_ASM3036279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030362795.1_ASM3036279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:40:48,147] [INFO] Task succeeded: fastANI [2024-01-24 14:40:48,159] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 14:40:48,159] [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_003314995.1 s__Pseudochrobactrum asaccharolyticum 90.1933 1179 1468 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 - GCA_900470285.1 s__Pseudochrobactrum sp900470285 86.3737 1021 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum 95.0 97.83 97.83 0.89 0.89 2 - GCF_008801715.1 s__Pseudochrobactrum saccharolyticum 86.1876 1001 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Pseudochrobactrum 95.0 96.83 96.24 0.94 0.92 10 - GCF_014205685.1 s__Paenochrobactrum gallinarii 78.4929 344 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paenochrobactrum 95.0 N/A N/A N/A N/A 1 - GCF_003049685.1 s__Ochrobactrum_A pituitosa 77.8844 298 1468 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_006476605.1 s__Ochrobactrum_A gallinifaecis 77.7551 267 1468 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_002252525.1 s__Ochrobactrum_A pseudogrignonensis 77.7244 300 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A 95.0 97.50 96.15 0.90 0.81 34 - GCF_014397025.1 s__Ochrobactrum_A sp014397025 77.6026 252 1468 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 - GCA_900470195.1 s__Ochrobactrum sp900470195 77.2475 226 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum 95.0 99.22 97.63 0.95 0.85 7 - GCF_005938105.1 s__Ochrobactrum_B haematophila 77.0892 290 1468 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 - GCF_014189505.1 s__Phyllobacterium sp014189505 76.892 169 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium 95.0 N/A N/A N/A N/A 1 - GCA_900472835.1 s__Phyllobacterium sp900472835 76.8811 182 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium 95.0 99.91 98.56 0.99 0.96 30 - GCF_001558695.1 s__Paramesorhizobium deserti 76.6353 137 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium 95.0 N/A N/A N/A N/A 1 - GCF_004343585.1 s__Neorhizobium sp004343585 76.6032 106 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium 95.0 N/A N/A N/A N/A 1 - GCF_002980495.1 s__Paramesorhizobium phragmitis 76.3551 172 1468 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 14:40:48,161] [INFO] GTDB search result was written to GCF_030362795.1_ASM3036279v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:40:48,161] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:40:48,164] [INFO] DFAST_QC result json was written to GCF_030362795.1_ASM3036279v1_genomic.fna/dqc_result.json [2024-01-24 14:40:48,165] [INFO] DFAST_QC completed! [2024-01-24 14:40:48,165] [INFO] Total running time: 0h1m19s