[2024-01-24 13:32:35,059] [INFO] DFAST_QC pipeline started. [2024-01-24 13:32:35,061] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:32:35,061] [INFO] DQC Reference Directory: /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference [2024-01-24 13:32:36,492] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:32:36,493] [INFO] Task started: Prodigal [2024-01-24 13:32:36,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bae5e7d-6c2a-4585-9c8d-f9bbd3377149/GCF_000402035.1_ASM40203v1_genomic.fna.gz | prodigal -d GCF_000402035.1_ASM40203v1_genomic.fna/cds.fna -a GCF_000402035.1_ASM40203v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:32:58,889] [INFO] Task succeeded: Prodigal [2024-01-24 13:32:58,889] [INFO] Task started: HMMsearch [2024-01-24 13:32:58,889] [INFO] Running command: hmmsearch --tblout GCF_000402035.1_ASM40203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/reference_markers.hmm GCF_000402035.1_ASM40203v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:32:59,394] [INFO] Task succeeded: HMMsearch [2024-01-24 13:32:59,396] [INFO] Found 6/6 markers. [2024-01-24 13:32:59,503] [INFO] Query marker FASTA was written to GCF_000402035.1_ASM40203v1_genomic.fna/markers.fasta [2024-01-24 13:32:59,504] [INFO] Task started: Blastn [2024-01-24 13:32:59,504] [INFO] Running command: blastn -query GCF_000402035.1_ASM40203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/reference_markers.fasta -out GCF_000402035.1_ASM40203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:33:00,609] [INFO] Task succeeded: Blastn [2024-01-24 13:33:00,612] [INFO] Selected 18 target genomes. [2024-01-24 13:33:00,612] [INFO] Target genome list was writen to GCF_000402035.1_ASM40203v1_genomic.fna/target_genomes.txt [2024-01-24 13:33:00,632] [INFO] Task started: fastANI [2024-01-24 13:33:00,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bae5e7d-6c2a-4585-9c8d-f9bbd3377149/GCF_000402035.1_ASM40203v1_genomic.fna.gz --refList GCF_000402035.1_ASM40203v1_genomic.fna/target_genomes.txt --output GCF_000402035.1_ASM40203v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:33:36,011] [INFO] Task succeeded: fastANI [2024-01-24 13:33:36,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:33:36,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:33:36,028] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:33:36,029] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:33:36,029] [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 Caballeronia insecticola strain=RPE64 GCA_000402035.1 758793 758793 type True 100.0 2318 2320 95 conclusive Caballeronia ptereochthonis GCA_001545075.2 1777144 1777144 type True 88.6188 1741 2320 95 below_threshold Caballeronia novacaledonica strain=LMG 28615 GCA_900258035.1 1544861 1544861 type True 87.9073 1637 2320 95 below_threshold Caballeronia calidae GCA_900044055.2 1777139 1777139 type True 87.868 1690 2320 95 below_threshold Caballeronia pedi GCA_001544915.2 1777141 1777141 type True 87.8305 1809 2320 95 below_threshold Caballeronia temeraria GCA_001544795.2 1777137 1777137 type True 87.648 1695 2320 95 below_threshold Caballeronia arvi GCA_001544695.2 1777135 1777135 type True 87.3399 1748 2320 95 below_threshold Caballeronia catudaia GCA_001544755.2 1777136 1777136 type True 87.3373 1640 2320 95 below_threshold Caballeronia cordobensis GCA_001544575.2 1353886 1353886 type True 87.3009 1758 2320 95 below_threshold Caballeronia cordobensis strain=LMG 27620 GCA_001278535.1 1353886 1353886 type True 87.2962 1792 2320 95 below_threshold Caballeronia fortuita GCA_001544835.2 1777138 1777138 type True 87.2486 1664 2320 95 below_threshold Caballeronia zhejiangensis strain=OP-1 GCA_000698575.1 871203 871203 type True 87.2181 1684 2320 95 below_threshold Caballeronia hypogeia GCA_001544875.2 1777140 1777140 type True 87.0731 1709 2320 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 81.2099 1280 2320 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.0734 1099 2320 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.5313 1072 2320 95 below_threshold Paraburkholderia silviterrae strain=4M-K11 GCA_004353915.1 2528715 2528715 type True 80.4786 1030 2320 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 80.0712 994 2320 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:33:36,030] [INFO] DFAST Taxonomy check result was written to GCF_000402035.1_ASM40203v1_genomic.fna/tc_result.tsv [2024-01-24 13:33:36,031] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:33:36,031] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:33:36,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/checkm_data [2024-01-24 13:33:36,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:33:36,103] [INFO] Task started: CheckM [2024-01-24 13:33:36,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000402035.1_ASM40203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000402035.1_ASM40203v1_genomic.fna/checkm_input GCF_000402035.1_ASM40203v1_genomic.fna/checkm_result [2024-01-24 13:34:41,708] [INFO] Task succeeded: CheckM [2024-01-24 13:34:41,709] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:34:41,730] [INFO] ===== Completeness check finished ===== [2024-01-24 13:34:41,731] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:34:41,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000402035.1_ASM40203v1_genomic.fna/markers.fasta) [2024-01-24 13:34:41,732] [INFO] Task started: Blastn [2024-01-24 13:34:41,732] [INFO] Running command: blastn -query GCF_000402035.1_ASM40203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga48fee59-a014-4d20-9da0-c4a1da1ed8ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000402035.1_ASM40203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:34:43,670] [INFO] Task succeeded: Blastn [2024-01-24 13:34:43,675] [INFO] Selected 14 target genomes. [2024-01-24 13:34:43,675] [INFO] Target genome list was writen to GCF_000402035.1_ASM40203v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:34:43,721] [INFO] Task started: fastANI [2024-01-24 13:34:43,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bae5e7d-6c2a-4585-9c8d-f9bbd3377149/GCF_000402035.1_ASM40203v1_genomic.fna.gz --refList GCF_000402035.1_ASM40203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000402035.1_ASM40203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:35:11,286] [INFO] Task succeeded: fastANI [2024-01-24 13:35:11,311] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:35:11,311] [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_000402035.1 s__Caballeronia insecticola 100.0 2318 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 conclusive GCA_001544595.2 s__Caballeronia peredens 92.4133 1745 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001545075.1 s__Caballeronia ptereochthonis 88.6106 1742 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCA_001189345.1 s__Caballeronia kirkii_B 88.0504 1041 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_900258035.1 s__Caballeronia novacaledonica 87.9156 1636 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_900044055.2 s__Caballeronia calidae 87.863 1690 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCA_000648925.1 s__Caballeronia jiangsuensis 87.837 1749 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 96.41 96.41 0.81 0.81 2 - GCA_001189335.2 s__Caballeronia schumannianae_A 87.8231 554 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.68 95.68 0.80 0.80 2 - GCF_001544915.2 s__Caballeronia pedi 87.8226 1811 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_018408855.1 s__Caballeronia sp018408855 87.8012 1830 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.23 98.23 0.88 0.88 2 - GCA_001580565.1 s__Caballeronia megalochromosomata 87.6614 1767 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544795.2 s__Caballeronia temeraria 87.6498 1694 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544575.2 s__Caballeronia cordobensis 87.301 1758 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.18 97.54 0.94 0.91 5 - GCF_001544875.2 s__Caballeronia hypogeia 87.0805 1708 2320 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:35:11,313] [INFO] GTDB search result was written to GCF_000402035.1_ASM40203v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:35:11,313] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:35:11,317] [INFO] DFAST_QC result json was written to GCF_000402035.1_ASM40203v1_genomic.fna/dqc_result.json [2024-01-24 13:35:11,317] [INFO] DFAST_QC completed! [2024-01-24 13:35:11,317] [INFO] Total running time: 0h2m36s