[2024-01-25 18:49:05,667] [INFO] DFAST_QC pipeline started. [2024-01-25 18:49:05,668] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:49:05,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference [2024-01-25 18:49:06,844] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:49:06,844] [INFO] Task started: Prodigal [2024-01-25 18:49:06,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg100f9817-6eec-4382-8c22-2f53a5fc9a65/GCF_001028175.1_ASM102817v1_genomic.fna.gz | prodigal -d GCF_001028175.1_ASM102817v1_genomic.fna/cds.fna -a GCF_001028175.1_ASM102817v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:49:32,311] [INFO] Task succeeded: Prodigal [2024-01-25 18:49:32,312] [INFO] Task started: HMMsearch [2024-01-25 18:49:32,312] [INFO] Running command: hmmsearch --tblout GCF_001028175.1_ASM102817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/reference_markers.hmm GCF_001028175.1_ASM102817v1_genomic.fna/protein.faa > /dev/null [2024-01-25 18:49:32,678] [INFO] Task succeeded: HMMsearch [2024-01-25 18:49:32,679] [INFO] Found 6/6 markers. [2024-01-25 18:49:32,755] [INFO] Query marker FASTA was written to GCF_001028175.1_ASM102817v1_genomic.fna/markers.fasta [2024-01-25 18:49:32,755] [INFO] Task started: Blastn [2024-01-25 18:49:32,755] [INFO] Running command: blastn -query GCF_001028175.1_ASM102817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/reference_markers.fasta -out GCF_001028175.1_ASM102817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:49:33,581] [INFO] Task succeeded: Blastn [2024-01-25 18:49:33,584] [INFO] Selected 18 target genomes. [2024-01-25 18:49:33,584] [INFO] Target genome list was writen to GCF_001028175.1_ASM102817v1_genomic.fna/target_genomes.txt [2024-01-25 18:49:33,593] [INFO] Task started: fastANI [2024-01-25 18:49:33,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg100f9817-6eec-4382-8c22-2f53a5fc9a65/GCF_001028175.1_ASM102817v1_genomic.fna.gz --refList GCF_001028175.1_ASM102817v1_genomic.fna/target_genomes.txt --output GCF_001028175.1_ASM102817v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:50:04,790] [INFO] Task succeeded: fastANI [2024-01-25 18:50:04,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:50:04,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:50:04,802] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold) [2024-01-25 18:50:04,802] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 18:50:04,802] [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 mineralivorans strain=PML1(12) GCA_001028175.1 2010198 2010198 type True 100.0 2963 2976 95 conclusive Caballeronia udeis GCA_001544555.2 1232866 1232866 type True 87.7611 1986 2976 95 below_threshold Caballeronia telluris GCA_001544495.2 326475 326475 type True 81.2765 1068 2976 95 below_threshold Caballeronia choica GCA_001544535.2 326476 326476 type True 81.2537 1114 2976 95 below_threshold Caballeronia terrestris GCA_001544515.2 1226301 1226301 type True 81.2203 1071 2976 95 below_threshold Caballeronia humi GCA_001544475.2 326474 326474 type True 81.2075 1072 2976 95 below_threshold Caballeronia glathei strain=LMG 14190 GCA_000751215.2 60547 60547 type True 81.1041 1138 2976 95 below_threshold Caballeronia glathei strain=DSM 50014 GCA_000698595.1 60547 60547 type True 81.0339 1119 2976 95 below_threshold Caballeronia arationis GCA_001544975.2 1777142 1777142 type True 80.9784 1115 2976 95 below_threshold Caballeronia zhejiangensis strain=OP-1 GCA_000698575.1 871203 871203 type True 80.3028 993 2976 95 below_threshold Paraburkholderia panacisoli strain=DCY113 GCA_008369935.1 2603818 2603818 type True 79.8301 1065 2976 95 below_threshold Paraburkholderia ginsengisoli strain=NBRC 100965 GCA_000739735.1 311231 311231 type True 79.8072 914 2976 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 79.7361 874 2976 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 79.5341 843 2976 95 below_threshold Paraburkholderia fynbosensis strain=LMG 27177 GCA_902859935.1 1200993 1200993 type True 79.5082 979 2976 95 below_threshold Paraburkholderia kirstenboschensis strain=KB15 GCA_001636975.1 1245436 1245436 type True 79.3729 743 2976 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 79.3417 960 2976 95 below_threshold Burkholderia perseverans strain=INN12 GCA_022870505.1 2615214 2615214 type True 78.7304 749 2976 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:50:04,806] [INFO] DFAST Taxonomy check result was written to GCF_001028175.1_ASM102817v1_genomic.fna/tc_result.tsv [2024-01-25 18:50:04,807] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:50:04,807] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:50:04,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/checkm_data [2024-01-25 18:50:04,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:50:04,899] [INFO] Task started: CheckM [2024-01-25 18:50:04,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001028175.1_ASM102817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001028175.1_ASM102817v1_genomic.fna/checkm_input GCF_001028175.1_ASM102817v1_genomic.fna/checkm_result [2024-01-25 18:51:14,539] [INFO] Task succeeded: CheckM [2024-01-25 18:51:14,540] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.38% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:51:14,586] [INFO] ===== Completeness check finished ===== [2024-01-25 18:51:14,586] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:51:14,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001028175.1_ASM102817v1_genomic.fna/markers.fasta) [2024-01-25 18:51:14,586] [INFO] Task started: Blastn [2024-01-25 18:51:14,587] [INFO] Running command: blastn -query GCF_001028175.1_ASM102817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8236994f-3ea1-455f-99b8-b8517b8e50ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_001028175.1_ASM102817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:51:16,133] [INFO] Task succeeded: Blastn [2024-01-25 18:51:16,136] [INFO] Selected 7 target genomes. [2024-01-25 18:51:16,136] [INFO] Target genome list was writen to GCF_001028175.1_ASM102817v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:51:16,144] [INFO] Task started: fastANI [2024-01-25 18:51:16,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg100f9817-6eec-4382-8c22-2f53a5fc9a65/GCF_001028175.1_ASM102817v1_genomic.fna.gz --refList GCF_001028175.1_ASM102817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001028175.1_ASM102817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:51:32,775] [INFO] Task succeeded: fastANI [2024-01-25 18:51:32,781] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:51:32,781] [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_001028175.1 s__Caballeronia mineralivorans 100.0 2963 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.87 95.86 0.82 0.81 4 conclusive GCF_001544555.2 s__Caballeronia udeis 87.7581 1987 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.62 95.53 0.77 0.76 8 - GCF_018449515.1 s__Caballeronia sp018449515 87.681 1730 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_002220365.1 s__Caballeronia sordidicola_C 87.445 1776 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_011493005.1 s__Caballeronia sp011493005 87.3967 1785 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.62 99.62 0.93 0.93 2 - GCF_000729995.1 s__Caballeronia sordidicola_A 87.3913 1916 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_009766085.1 s__Caballeronia sp009766085 87.3575 1769 2976 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 18:51:32,783] [INFO] GTDB search result was written to GCF_001028175.1_ASM102817v1_genomic.fna/result_gtdb.tsv [2024-01-25 18:51:32,783] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:51:32,789] [INFO] DFAST_QC result json was written to GCF_001028175.1_ASM102817v1_genomic.fna/dqc_result.json [2024-01-25 18:51:32,789] [INFO] DFAST_QC completed! [2024-01-25 18:51:32,789] [INFO] Total running time: 0h2m27s