[2024-01-25 19:48:50,760] [INFO] DFAST_QC pipeline started. [2024-01-25 19:48:50,762] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:48:50,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference [2024-01-25 19:48:51,912] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:48:51,913] [INFO] Task started: Prodigal [2024-01-25 19:48:51,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5d83c4d-0c0d-49f3-bfd1-4b1d9ce9fb9f/GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna.gz | prodigal -d GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/cds.fna -a GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:49:14,938] [INFO] Task succeeded: Prodigal [2024-01-25 19:49:14,939] [INFO] Task started: HMMsearch [2024-01-25 19:49:14,939] [INFO] Running command: hmmsearch --tblout GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/reference_markers.hmm GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/protein.faa > /dev/null [2024-01-25 19:49:15,246] [INFO] Task succeeded: HMMsearch [2024-01-25 19:49:15,247] [INFO] Found 6/6 markers. [2024-01-25 19:49:15,316] [INFO] Query marker FASTA was written to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/markers.fasta [2024-01-25 19:49:15,317] [INFO] Task started: Blastn [2024-01-25 19:49:15,317] [INFO] Running command: blastn -query GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/reference_markers.fasta -out GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:49:16,320] [INFO] Task succeeded: Blastn [2024-01-25 19:49:16,324] [INFO] Selected 14 target genomes. [2024-01-25 19:49:16,324] [INFO] Target genome list was writen to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/target_genomes.txt [2024-01-25 19:49:16,336] [INFO] Task started: fastANI [2024-01-25 19:49:16,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d83c4d-0c0d-49f3-bfd1-4b1d9ce9fb9f/GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna.gz --refList GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/target_genomes.txt --output GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:49:45,230] [INFO] Task succeeded: fastANI [2024-01-25 19:49:45,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:49:45,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:49:45,239] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold) [2024-01-25 19:49:45,239] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:49:45,240] [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 temeraria GCA_001544795.2 1777137 1777137 type True 100.0 2704 2713 95 conclusive Caballeronia zhejiangensis strain=OP-1 GCA_000698575.1 871203 871203 type True 90.7289 1934 2713 95 below_threshold Caballeronia glebae GCA_001545035.2 1777143 1777143 type True 90.3961 1933 2713 95 below_threshold Caballeronia fortuita GCA_001544835.2 1777138 1777138 type True 89.9994 1961 2713 95 below_threshold Caballeronia novacaledonica strain=LMG 28615 GCA_900258035.1 1544861 1544861 type True 89.6984 1725 2713 95 below_threshold Caballeronia calidae GCA_900044055.2 1777139 1777139 type True 89.0399 1849 2713 95 below_threshold Caballeronia pedi GCA_001544915.2 1777141 1777141 type True 88.9124 1912 2713 95 below_threshold Caballeronia cordobensis GCA_001544575.2 1353886 1353886 type True 88.3125 1892 2713 95 below_threshold Caballeronia cordobensis strain=LMG 27620 GCA_001278535.1 1353886 1353886 type True 88.1954 1966 2713 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 81.3037 1312 2713 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 81.128 982 2713 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.0868 1144 2713 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 81.0178 996 2713 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.6875 1103 2713 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:49:45,241] [INFO] DFAST Taxonomy check result was written to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/tc_result.tsv [2024-01-25 19:49:45,241] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:49:45,242] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:49:45,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/checkm_data [2024-01-25 19:49:45,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:49:45,319] [INFO] Task started: CheckM [2024-01-25 19:49:45,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/checkm_input GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/checkm_result [2024-01-25 19:50:59,030] [INFO] Task succeeded: CheckM [2024-01-25 19:50:59,030] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:50:59,054] [INFO] ===== Completeness check finished ===== [2024-01-25 19:50:59,054] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:50:59,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/markers.fasta) [2024-01-25 19:50:59,055] [INFO] Task started: Blastn [2024-01-25 19:50:59,055] [INFO] Running command: blastn -query GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a579a-a463-4382-b9ba-ec57c4745188/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:51:01,065] [INFO] Task succeeded: Blastn [2024-01-25 19:51:01,067] [INFO] Selected 12 target genomes. [2024-01-25 19:51:01,067] [INFO] Target genome list was writen to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:51:01,078] [INFO] Task started: fastANI [2024-01-25 19:51:01,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d83c4d-0c0d-49f3-bfd1-4b1d9ce9fb9f/GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna.gz --refList GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/target_genomes_gtdb.txt --output GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:51:27,581] [INFO] Task succeeded: fastANI [2024-01-25 19:51:27,589] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:51:27,589] [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_001544795.2 s__Caballeronia temeraria 100.0 2704 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 conclusive GCF_000698575.1 s__Caballeronia zhejiangensis 90.74 1933 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.44 99.18 0.93 0.92 4 - GCF_001545035.1 s__Caballeronia glebae 90.3805 1935 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544835.2 s__Caballeronia fortuita 89.9986 1961 2713 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 89.6943 1726 2713 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 89.5242 1887 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 96.41 96.41 0.81 0.81 2 - GCA_001580565.1 s__Caballeronia megalochromosomata 89.2971 1906 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCA_001544655.2 s__Caballeronia turbans 89.1072 1855 2713 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 89.0272 1851 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544915.2 s__Caballeronia pedi 88.9133 1912 2713 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 88.7909 1991 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.23 98.23 0.88 0.88 2 - GCF_001544575.2 s__Caballeronia cordobensis 88.2834 1897 2713 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.18 97.54 0.94 0.91 5 - -------------------------------------------------------------------------------- [2024-01-25 19:51:27,593] [INFO] GTDB search result was written to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/result_gtdb.tsv [2024-01-25 19:51:27,593] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:51:27,596] [INFO] DFAST_QC result json was written to GCF_001544795.2_Burkholderia_sp._LMG_29319_genomic.fna/dqc_result.json [2024-01-25 19:51:27,596] [INFO] DFAST_QC completed! [2024-01-25 19:51:27,597] [INFO] Total running time: 0h2m37s