[2024-01-24 14:05:01,032] [INFO] DFAST_QC pipeline started. [2024-01-24 14:05:01,034] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:05:01,034] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference [2024-01-24 14:05:02,234] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:05:02,235] [INFO] Task started: Prodigal [2024-01-24 14:05:02,235] [INFO] Running command: gunzip -c /var/lib/cwl/stgc903de15-e1c4-4314-8358-dddff5b474d1/GCF_016100835.1_ASM1610083v1_genomic.fna.gz | prodigal -d GCF_016100835.1_ASM1610083v1_genomic.fna/cds.fna -a GCF_016100835.1_ASM1610083v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:05:10,339] [INFO] Task succeeded: Prodigal [2024-01-24 14:05:10,339] [INFO] Task started: HMMsearch [2024-01-24 14:05:10,339] [INFO] Running command: hmmsearch --tblout GCF_016100835.1_ASM1610083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/reference_markers.hmm GCF_016100835.1_ASM1610083v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:05:10,528] [INFO] Task succeeded: HMMsearch [2024-01-24 14:05:10,529] [INFO] Found 6/6 markers. [2024-01-24 14:05:10,551] [INFO] Query marker FASTA was written to GCF_016100835.1_ASM1610083v1_genomic.fna/markers.fasta [2024-01-24 14:05:10,552] [INFO] Task started: Blastn [2024-01-24 14:05:10,552] [INFO] Running command: blastn -query GCF_016100835.1_ASM1610083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/reference_markers.fasta -out GCF_016100835.1_ASM1610083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:05:11,232] [INFO] Task succeeded: Blastn [2024-01-24 14:05:11,235] [INFO] Selected 27 target genomes. [2024-01-24 14:05:11,235] [INFO] Target genome list was writen to GCF_016100835.1_ASM1610083v1_genomic.fna/target_genomes.txt [2024-01-24 14:05:11,396] [INFO] Task started: fastANI [2024-01-24 14:05:11,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgc903de15-e1c4-4314-8358-dddff5b474d1/GCF_016100835.1_ASM1610083v1_genomic.fna.gz --refList GCF_016100835.1_ASM1610083v1_genomic.fna/target_genomes.txt --output GCF_016100835.1_ASM1610083v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:05:22,729] [INFO] Task succeeded: fastANI [2024-01-24 14:05:22,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:05:22,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:05:22,738] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold) [2024-01-24 14:05:22,738] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 14:05:22,739] [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 Bartonella apis strain=PEB0122 GCA_001952075.1 1686310 1686310 type True 86.2597 729 923 95 below_threshold Brucella suis strain=1330 GCA_000223195.1 29461 29461 suspected-type True 76.3257 53 923 95 below_threshold Brucella suis strain=1330 GCA_000007505.1 29461 29461 suspected-type True 76.3257 53 923 95 below_threshold Brucella suis strain=NCTC10316 GCA_900460605.1 29461 29461 suspected-type True 76.3213 53 923 95 below_threshold Brucella melitensis strain=16M GCA_000160295.1 29459 29459 suspected-type True 76.2298 56 923 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 76.198 63 923 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 76.198 63 923 95 below_threshold Brucella melitensis strain=16M GCA_000250795.2 29459 29459 suspected-type True 76.1297 53 923 95 below_threshold Paenochrobactrum gallinarii strain=DSM 22336 GCA_014205685.1 643673 643673 type True 76.1031 64 923 95 below_threshold Pseudochrobactrum saccharolyticum strain=DSM 25620 GCA_014203195.1 354352 354352 type True 76.0755 61 923 95 below_threshold Pseudochrobactrum saccharolyticum strain=CCUG 33852 GCA_008801715.1 354352 354352 type True 76.0709 61 923 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:05:22,740] [INFO] DFAST Taxonomy check result was written to GCF_016100835.1_ASM1610083v1_genomic.fna/tc_result.tsv [2024-01-24 14:05:22,740] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:05:22,741] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:05:22,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/checkm_data [2024-01-24 14:05:22,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:05:22,769] [INFO] Task started: CheckM [2024-01-24 14:05:22,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016100835.1_ASM1610083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016100835.1_ASM1610083v1_genomic.fna/checkm_input GCF_016100835.1_ASM1610083v1_genomic.fna/checkm_result [2024-01-24 14:05:52,859] [INFO] Task succeeded: CheckM [2024-01-24 14:05:52,860] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:05:52,881] [INFO] ===== Completeness check finished ===== [2024-01-24 14:05:52,882] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:05:52,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016100835.1_ASM1610083v1_genomic.fna/markers.fasta) [2024-01-24 14:05:52,882] [INFO] Task started: Blastn [2024-01-24 14:05:52,882] [INFO] Running command: blastn -query GCF_016100835.1_ASM1610083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf6979d9-0911-48b4-9f64-1e649aea02b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016100835.1_ASM1610083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:05:54,053] [INFO] Task succeeded: Blastn [2024-01-24 14:05:54,059] [INFO] Selected 8 target genomes. [2024-01-24 14:05:54,060] [INFO] Target genome list was writen to GCF_016100835.1_ASM1610083v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:05:54,068] [INFO] Task started: fastANI [2024-01-24 14:05:54,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgc903de15-e1c4-4314-8358-dddff5b474d1/GCF_016100835.1_ASM1610083v1_genomic.fna.gz --refList GCF_016100835.1_ASM1610083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016100835.1_ASM1610083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:05:58,808] [INFO] Task succeeded: fastANI [2024-01-24 14:05:58,815] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:05:58,815] [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_002007565.1 s__Bartonella apis_B 98.2704 881 923 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella 95.0 98.26 98.25 0.96 0.95 4 conclusive GCF_016102285.1 s__Bartonella sp016102285 86.7224 714 923 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella 95.0 N/A N/A N/A N/A 1 - GCF_016100455.1 s__Bartonella sp016100455 86.6654 719 923 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella 95.0 N/A N/A N/A N/A 1 - GCF_002007485.1 s__Bartonella apis_A 86.616 702 923 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella 95.0 97.35 97.25 0.96 0.95 12 - GCF_001952075.1 s__Bartonella apis 86.2597 729 923 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella 95.0 97.04 95.90 0.96 0.95 9 - -------------------------------------------------------------------------------- [2024-01-24 14:05:58,817] [INFO] GTDB search result was written to GCF_016100835.1_ASM1610083v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:05:58,818] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:05:58,822] [INFO] DFAST_QC result json was written to GCF_016100835.1_ASM1610083v1_genomic.fna/dqc_result.json [2024-01-24 14:05:58,823] [INFO] DFAST_QC completed! [2024-01-24 14:05:58,823] [INFO] Total running time: 0h0m58s