[2024-01-24 11:09:50,715] [INFO] DFAST_QC pipeline started. [2024-01-24 11:09:50,717] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:09:50,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference [2024-01-24 11:09:53,302] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:09:53,303] [INFO] Task started: Prodigal [2024-01-24 11:09:53,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9664f77-d100-4180-aefe-dd0a092b482b/GCF_900625035.1_DSM_17516T_genomic.fna.gz | prodigal -d GCF_900625035.1_DSM_17516T_genomic.fna/cds.fna -a GCF_900625035.1_DSM_17516T_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:10:19,298] [INFO] Task succeeded: Prodigal [2024-01-24 11:10:19,299] [INFO] Task started: HMMsearch [2024-01-24 11:10:19,299] [INFO] Running command: hmmsearch --tblout GCF_900625035.1_DSM_17516T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/reference_markers.hmm GCF_900625035.1_DSM_17516T_genomic.fna/protein.faa > /dev/null [2024-01-24 11:10:19,615] [INFO] Task succeeded: HMMsearch [2024-01-24 11:10:19,617] [INFO] Found 6/6 markers. [2024-01-24 11:10:19,673] [INFO] Query marker FASTA was written to GCF_900625035.1_DSM_17516T_genomic.fna/markers.fasta [2024-01-24 11:10:19,674] [INFO] Task started: Blastn [2024-01-24 11:10:19,674] [INFO] Running command: blastn -query GCF_900625035.1_DSM_17516T_genomic.fna/markers.fasta -db /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/reference_markers.fasta -out GCF_900625035.1_DSM_17516T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:10:20,562] [INFO] Task succeeded: Blastn [2024-01-24 11:10:20,567] [INFO] Selected 20 target genomes. [2024-01-24 11:10:20,567] [INFO] Target genome list was writen to GCF_900625035.1_DSM_17516T_genomic.fna/target_genomes.txt [2024-01-24 11:10:20,579] [INFO] Task started: fastANI [2024-01-24 11:10:20,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9664f77-d100-4180-aefe-dd0a092b482b/GCF_900625035.1_DSM_17516T_genomic.fna.gz --refList GCF_900625035.1_DSM_17516T_genomic.fna/target_genomes.txt --output GCF_900625035.1_DSM_17516T_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:10:53,803] [INFO] Task succeeded: fastANI [2024-01-24 11:10:53,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:10:53,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:10:53,826] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold) [2024-01-24 11:10:53,827] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:10:53,827] [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 Pseudomonas cedrina subsp. cedrina GCA_900625035.1 76762 651740 type True 100.0 2140 2141 95 conclusive Pseudomonas cedrina subsp. cedrina strain=DSM 17516 GCA_001983175.1 76762 651740 type True 99.9977 2132 2141 95 conclusive Pseudomonas marginalis strain=ICMP 3553 GCA_001645105.1 298 298 suspected-type True 89.3856 1652 2141 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 89.3516 1575 2141 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 89.2275 1659 2141 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 89.2249 1635 2141 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 89.2105 1676 2141 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 89.1946 1647 2141 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 89.1666 1614 2141 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 89.1388 1608 2141 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 89.1164 1633 2141 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 89.1084 1592 2141 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 88.9453 1602 2141 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 88.9003 1618 2141 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.5455 1677 2141 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_007858235.1 359110 359110 type True 87.9812 1471 2141 95 below_threshold Pseudomonas extremaustralis GCA_900625045.1 359110 359110 type True 87.9698 1468 2141 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_900102035.1 359110 359110 type True 87.9264 1497 2141 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.6951 1370 2141 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.9359 1298 2141 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:10:53,829] [INFO] DFAST Taxonomy check result was written to GCF_900625035.1_DSM_17516T_genomic.fna/tc_result.tsv [2024-01-24 11:10:53,829] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:10:53,830] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:10:53,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/checkm_data [2024-01-24 11:10:53,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:10:53,891] [INFO] Task started: CheckM [2024-01-24 11:10:53,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900625035.1_DSM_17516T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900625035.1_DSM_17516T_genomic.fna/checkm_input GCF_900625035.1_DSM_17516T_genomic.fna/checkm_result [2024-01-24 11:12:05,766] [INFO] Task succeeded: CheckM [2024-01-24 11:12:05,767] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:12:05,789] [INFO] ===== Completeness check finished ===== [2024-01-24 11:12:05,789] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:12:05,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900625035.1_DSM_17516T_genomic.fna/markers.fasta) [2024-01-24 11:12:05,791] [INFO] Task started: Blastn [2024-01-24 11:12:05,791] [INFO] Running command: blastn -query GCF_900625035.1_DSM_17516T_genomic.fna/markers.fasta -db /var/lib/cwl/stg26acb321-a378-4ec3-bfb2-cc17d11c6890/dqc_reference/reference_markers_gtdb.fasta -out GCF_900625035.1_DSM_17516T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:12:07,215] [INFO] Task succeeded: Blastn [2024-01-24 11:12:07,223] [INFO] Selected 20 target genomes. [2024-01-24 11:12:07,224] [INFO] Target genome list was writen to GCF_900625035.1_DSM_17516T_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:12:07,259] [INFO] Task started: fastANI [2024-01-24 11:12:07,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9664f77-d100-4180-aefe-dd0a092b482b/GCF_900625035.1_DSM_17516T_genomic.fna.gz --refList GCF_900625035.1_DSM_17516T_genomic.fna/target_genomes_gtdb.txt --output GCF_900625035.1_DSM_17516T_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:12:40,385] [INFO] Task succeeded: fastANI [2024-01-24 11:12:40,411] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:12:40,412] [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_001983175.1 s__Pseudomonas_E cedrina 99.9977 2132 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 conclusive GCF_012844475.1 s__Pseudomonas_E sp012844475 94.3957 1622 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCA_016937595.1 s__Pseudomonas_E fulgida 92.7299 1171 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_001186335.1 s__Pseudomonas_E trivialis_B 89.7013 1715 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.34 95.31 0.86 0.86 8 - GCF_001645105.1 s__Pseudomonas_E marginalis_B 89.3643 1655 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 - GCF_900103345.1 s__Pseudomonas_E azotoformans 89.2285 1674 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.97 95.87 0.94 0.87 9 - GCF_001579805.1 s__Pseudomonas_E azotoformans_A 89.1975 1665 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.75 96.24 0.87 0.84 8 - GCF_001870465.1 s__Pseudomonas_E extremorientalis 89.1418 1608 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.37 98.13 0.91 0.89 29 - GCF_900111895.1 s__Pseudomonas_E simiae 88.9716 1598 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.45 99.32 0.95 0.92 20 - GCF_003097075.1 s__Pseudomonas_E sp003097075 88.8285 1578 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.77 98.77 0.94 0.94 2 - GCF_900580675.1 s__Pseudomonas_E sp900580675 88.5648 1516 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_002843605.1 s__Pseudomonas_E sp002843605 88.5393 1609 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.70 97.45 0.92 0.91 7 - GCF_900591205.1 s__Pseudomonas_E sp900591205 88.336 1608 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_001439815.1 s__Pseudomonas_E orientalis 88.1907 1550 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.01 96.05 0.91 0.89 6 - GCF_004682045.1 s__Pseudomonas_E nabeulensis 88.0293 1497 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.61 95.59 0.85 0.85 3 - GCF_019139815.1 s__Pseudomonas_E sp900005815 88.0073 1604 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.55 99.31 0.95 0.92 7 - GCF_900102035.1 s__Pseudomonas_E extremaustralis 87.9442 1495 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.74 98.99 0.98 0.92 5 - GCF_002837185.1 s__Pseudomonas_E fluorescens_AM 87.6261 1484 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.23 99.16 0.96 0.94 7 - GCF_003851495.1 s__Pseudomonas_E fluorescens_BB 87.2172 1526 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.3929 98.85 97.70 0.94 0.89 3 - GCF_000263715.2 s__Pseudomonas_E synxantha_A 87.1659 1508 2141 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.66 97.33 0.90 0.88 8 - -------------------------------------------------------------------------------- [2024-01-24 11:12:40,413] [INFO] GTDB search result was written to GCF_900625035.1_DSM_17516T_genomic.fna/result_gtdb.tsv [2024-01-24 11:12:40,414] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:12:40,418] [INFO] DFAST_QC result json was written to GCF_900625035.1_DSM_17516T_genomic.fna/dqc_result.json [2024-01-24 11:12:40,418] [INFO] DFAST_QC completed! [2024-01-24 11:12:40,418] [INFO] Total running time: 0h2m50s