[2024-01-25 20:03:20,855] [INFO] DFAST_QC pipeline started. [2024-01-25 20:03:20,856] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 20:03:20,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference [2024-01-25 20:03:22,013] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 20:03:22,014] [INFO] Task started: Prodigal [2024-01-25 20:03:22,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeb19ede-00ae-423c-a3ba-4de8c3696709/GCF_016102465.1_ASM1610246v1_genomic.fna.gz | prodigal -d GCF_016102465.1_ASM1610246v1_genomic.fna/cds.fna -a GCF_016102465.1_ASM1610246v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 20:03:28,803] [INFO] Task succeeded: Prodigal [2024-01-25 20:03:28,803] [INFO] Task started: HMMsearch [2024-01-25 20:03:28,803] [INFO] Running command: hmmsearch --tblout GCF_016102465.1_ASM1610246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/reference_markers.hmm GCF_016102465.1_ASM1610246v1_genomic.fna/protein.faa > /dev/null [2024-01-25 20:03:28,983] [INFO] Task succeeded: HMMsearch [2024-01-25 20:03:28,984] [INFO] Found 6/6 markers. [2024-01-25 20:03:29,006] [INFO] Query marker FASTA was written to GCF_016102465.1_ASM1610246v1_genomic.fna/markers.fasta [2024-01-25 20:03:29,006] [INFO] Task started: Blastn [2024-01-25 20:03:29,006] [INFO] Running command: blastn -query GCF_016102465.1_ASM1610246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/reference_markers.fasta -out GCF_016102465.1_ASM1610246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:03:29,640] [INFO] Task succeeded: Blastn [2024-01-25 20:03:29,645] [INFO] Selected 28 target genomes. [2024-01-25 20:03:29,646] [INFO] Target genome list was writen to GCF_016102465.1_ASM1610246v1_genomic.fna/target_genomes.txt [2024-01-25 20:03:29,663] [INFO] Task started: fastANI [2024-01-25 20:03:29,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb19ede-00ae-423c-a3ba-4de8c3696709/GCF_016102465.1_ASM1610246v1_genomic.fna.gz --refList GCF_016102465.1_ASM1610246v1_genomic.fna/target_genomes.txt --output GCF_016102465.1_ASM1610246v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 20:03:45,395] [INFO] Task succeeded: fastANI [2024-01-25 20:03:45,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 20:03:45,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 20:03:45,402] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold) [2024-01-25 20:03:45,402] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-25 20:03:45,403] [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 87.5489 727 878 95 below_threshold Pseudochrobactrum saccharolyticum strain=CCUG 33852 GCA_008801715.1 354352 354352 type True 76.3 66 878 95 below_threshold Pseudochrobactrum saccharolyticum strain=DSM 25620 GCA_014203195.1 354352 354352 type True 76.3 66 878 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 76.1926 63 878 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 76.1668 64 878 95 below_threshold Paenochrobactrum gallinarii strain=DSM 22336 GCA_014205685.1 643673 643673 type True 76.0867 64 878 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_003049685.2 571256 571256 type True 76.0691 60 878 95 below_threshold Brucella pituitosa strain=CCUG 50899 GCA_008801705.1 571256 571256 type True 76.0691 60 878 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 20:03:45,404] [INFO] DFAST Taxonomy check result was written to GCF_016102465.1_ASM1610246v1_genomic.fna/tc_result.tsv [2024-01-25 20:03:45,405] [INFO] ===== Taxonomy check completed ===== [2024-01-25 20:03:45,405] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 20:03:45,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/checkm_data [2024-01-25 20:03:45,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 20:03:45,433] [INFO] Task started: CheckM [2024-01-25 20:03:45,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016102465.1_ASM1610246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016102465.1_ASM1610246v1_genomic.fna/checkm_input GCF_016102465.1_ASM1610246v1_genomic.fna/checkm_result [2024-01-25 20:04:10,324] [INFO] Task succeeded: CheckM [2024-01-25 20:04:10,325] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 20:04:10,341] [INFO] ===== Completeness check finished ===== [2024-01-25 20:04:10,341] [INFO] ===== Start GTDB Search ===== [2024-01-25 20:04:10,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016102465.1_ASM1610246v1_genomic.fna/markers.fasta) [2024-01-25 20:04:10,343] [INFO] Task started: Blastn [2024-01-25 20:04:10,343] [INFO] Running command: blastn -query GCF_016102465.1_ASM1610246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcb8ac4a-7586-4892-b2f0-0780ab9f1ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016102465.1_ASM1610246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:04:11,402] [INFO] Task succeeded: Blastn [2024-01-25 20:04:11,404] [INFO] Selected 7 target genomes. [2024-01-25 20:04:11,405] [INFO] Target genome list was writen to GCF_016102465.1_ASM1610246v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 20:04:11,415] [INFO] Task started: fastANI [2024-01-25 20:04:11,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb19ede-00ae-423c-a3ba-4de8c3696709/GCF_016102465.1_ASM1610246v1_genomic.fna.gz --refList GCF_016102465.1_ASM1610246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016102465.1_ASM1610246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 20:04:15,661] [INFO] Task succeeded: fastANI [2024-01-25 20:04:15,666] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 20:04:15,667] [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_002007485.1 s__Bartonella apis_A 97.3641 831 878 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 conclusive GCF_016100455.1 s__Bartonella sp016100455 94.6232 807 878 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_016102285.1 s__Bartonella sp016102285 94.1393 806 878 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_001952075.1 s__Bartonella apis 87.5489 727 878 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 - GCF_002007565.1 s__Bartonella apis_B 86.4289 715 878 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 - GCA_002005325.1 s__Tokpelaia hoelldoblerii 76.0868 63 878 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 - -------------------------------------------------------------------------------- [2024-01-25 20:04:15,668] [INFO] GTDB search result was written to GCF_016102465.1_ASM1610246v1_genomic.fna/result_gtdb.tsv [2024-01-25 20:04:15,669] [INFO] ===== GTDB Search completed ===== [2024-01-25 20:04:15,671] [INFO] DFAST_QC result json was written to GCF_016102465.1_ASM1610246v1_genomic.fna/dqc_result.json [2024-01-25 20:04:15,671] [INFO] DFAST_QC completed! [2024-01-25 20:04:15,671] [INFO] Total running time: 0h0m55s