[2024-01-24 12:06:20,371] [INFO] DFAST_QC pipeline started. [2024-01-24 12:06:20,377] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:06:20,377] [INFO] DQC Reference Directory: /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference [2024-01-24 12:06:21,568] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:06:21,569] [INFO] Task started: Prodigal [2024-01-24 12:06:21,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg092ff638-25c6-4224-9648-3420516e9e5b/GCF_014205685.1_ASM1420568v1_genomic.fna.gz | prodigal -d GCF_014205685.1_ASM1420568v1_genomic.fna/cds.fna -a GCF_014205685.1_ASM1420568v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:06:31,229] [INFO] Task succeeded: Prodigal [2024-01-24 12:06:31,230] [INFO] Task started: HMMsearch [2024-01-24 12:06:31,230] [INFO] Running command: hmmsearch --tblout GCF_014205685.1_ASM1420568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/reference_markers.hmm GCF_014205685.1_ASM1420568v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:06:31,505] [INFO] Task succeeded: HMMsearch [2024-01-24 12:06:31,506] [INFO] Found 6/6 markers. [2024-01-24 12:06:31,535] [INFO] Query marker FASTA was written to GCF_014205685.1_ASM1420568v1_genomic.fna/markers.fasta [2024-01-24 12:06:31,536] [INFO] Task started: Blastn [2024-01-24 12:06:31,536] [INFO] Running command: blastn -query GCF_014205685.1_ASM1420568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/reference_markers.fasta -out GCF_014205685.1_ASM1420568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:06:32,238] [INFO] Task succeeded: Blastn [2024-01-24 12:06:32,242] [INFO] Selected 19 target genomes. [2024-01-24 12:06:32,242] [INFO] Target genome list was writen to GCF_014205685.1_ASM1420568v1_genomic.fna/target_genomes.txt [2024-01-24 12:06:32,249] [INFO] Task started: fastANI [2024-01-24 12:06:32,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg092ff638-25c6-4224-9648-3420516e9e5b/GCF_014205685.1_ASM1420568v1_genomic.fna.gz --refList GCF_014205685.1_ASM1420568v1_genomic.fna/target_genomes.txt --output GCF_014205685.1_ASM1420568v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:06:44,167] [INFO] Task succeeded: fastANI [2024-01-24 12:06:44,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:06:44,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:06:44,178] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold) [2024-01-24 12:06:44,178] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:06:44,178] [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 Paenochrobactrum gallinarii strain=DSM 22336 GCA_014205685.1 643673 643673 type True 100.0 1084 1089 95 conclusive Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 79.0467 353 1089 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 79.0427 355 1089 95 below_threshold Pseudochrobactrum saccharolyticum strain=CCUG 33852 GCA_008801715.1 354352 354352 type True 78.8813 334 1089 95 below_threshold Pseudochrobactrum saccharolyticum strain=DSM 25620 GCA_014203195.1 354352 354352 type True 78.8216 339 1089 95 below_threshold Brucella thiophenivorans strain=DSM 7216 GCA_002252445.1 571255 571255 type True 77.8603 260 1089 95 below_threshold Brucella pseudogrignonensis strain=CCUG 30717 GCA_002252525.1 419475 419475 type True 77.7689 269 1089 95 below_threshold [Ochrobactrum] quorumnocens strain=A44 GCA_002278035.1 271865 271865 type True 77.7277 246 1089 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_008801705.1 571256 571256 type True 77.7024 262 1089 95 below_threshold Brucella rhizosphaerae strain=PR17 GCA_002252475.1 571254 571254 type True 77.6774 234 1089 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_003049685.2 571256 571256 type True 77.6534 257 1089 95 below_threshold Brucella gallinifaecis strain=ISO 196 GCA_006476605.1 215590 215590 type True 77.6091 262 1089 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:06:44,180] [INFO] DFAST Taxonomy check result was written to GCF_014205685.1_ASM1420568v1_genomic.fna/tc_result.tsv [2024-01-24 12:06:44,180] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:06:44,181] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:06:44,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/checkm_data [2024-01-24 12:06:44,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:06:44,214] [INFO] Task started: CheckM [2024-01-24 12:06:44,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205685.1_ASM1420568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205685.1_ASM1420568v1_genomic.fna/checkm_input GCF_014205685.1_ASM1420568v1_genomic.fna/checkm_result [2024-01-24 12:07:17,251] [INFO] Task succeeded: CheckM [2024-01-24 12:07:17,253] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:07:17,274] [INFO] ===== Completeness check finished ===== [2024-01-24 12:07:17,275] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:07:17,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205685.1_ASM1420568v1_genomic.fna/markers.fasta) [2024-01-24 12:07:17,276] [INFO] Task started: Blastn [2024-01-24 12:07:17,276] [INFO] Running command: blastn -query GCF_014205685.1_ASM1420568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9739141-8a64-486a-a393-93a4786870d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205685.1_ASM1420568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:07:18,503] [INFO] Task succeeded: Blastn [2024-01-24 12:07:18,507] [INFO] Selected 22 target genomes. [2024-01-24 12:07:18,508] [INFO] Target genome list was writen to GCF_014205685.1_ASM1420568v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:07:18,577] [INFO] Task started: fastANI [2024-01-24 12:07:18,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg092ff638-25c6-4224-9648-3420516e9e5b/GCF_014205685.1_ASM1420568v1_genomic.fna.gz --refList GCF_014205685.1_ASM1420568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205685.1_ASM1420568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:07:33,720] [INFO] Task succeeded: fastANI [2024-01-24 12:07:33,736] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:07:33,736] [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_014205685.1 s__Paenochrobactrum gallinarii 100.0 1084 1089 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 conclusive GCF_003314995.1 s__Pseudochrobactrum asaccharolyticum 78.9385 373 1089 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_008801715.1 s__Pseudochrobactrum saccharolyticum 78.8868 334 1089 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 - GCA_900470285.1 s__Pseudochrobactrum sp900470285 78.5173 307 1089 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_002252505.1 s__Ochrobactrum_A grignonensis 78.028 276 1089 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_018798825.1 s__Ochrobactrum_A sp018798825 77.8678 271 1089 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_002252445.1 s__Ochrobactrum_A thiophenivorans 77.8603 260 1089 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 77.7596 269 1089 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_002278035.1 s__Ochrobactrum_A quorumnocens 77.7212 243 1089 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_002252475.1 s__Ochrobactrum_A rhizosphaerae 77.6774 234 1089 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_003049685.1 s__Ochrobactrum_A pituitosa 77.6426 257 1089 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 77.6153 260 1089 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_014138095.1 s__Ochrobactrum_B sp014138095 77.6041 268 1089 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 - GCA_900465685.1 s__Ochrobactrum_B sp900465685 77.5406 256 1089 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_003149535.1 s__Falsochrobactrum shanghaiense 77.5203 237 1089 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum 95.0 N/A N/A N/A N/A 1 - GCF_005938105.1 s__Ochrobactrum_B haematophila 77.4932 267 1089 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 - GCA_900473915.1 s__Ochrobactrum sp900473915 77.4809 233 1089 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum 95.0 N/A N/A N/A N/A 1 - GCF_003550135.1 s__Ochrobactrum_B haematophila_B 77.4321 235 1089 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 - GCA_002005325.1 s__Tokpelaia hoelldoblerii 76.6411 86 1089 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Tokpelaia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:07:33,739] [INFO] GTDB search result was written to GCF_014205685.1_ASM1420568v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:07:33,739] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:07:33,743] [INFO] DFAST_QC result json was written to GCF_014205685.1_ASM1420568v1_genomic.fna/dqc_result.json [2024-01-24 12:07:33,744] [INFO] DFAST_QC completed! [2024-01-24 12:07:33,744] [INFO] Total running time: 0h1m13s