[2024-01-24 10:47:06,591] [INFO] DFAST_QC pipeline started. [2024-01-24 10:47:06,599] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 10:47:06,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference [2024-01-24 10:47:12,684] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 10:47:12,818] [INFO] Task started: Prodigal [2024-01-24 10:47:12,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgd19f7981-76a1-476b-81d1-fdaddb89e026/GCF_026410085.1_ASM2641008v1_genomic.fna.gz | prodigal -d GCF_026410085.1_ASM2641008v1_genomic.fna/cds.fna -a GCF_026410085.1_ASM2641008v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 10:47:36,433] [INFO] Task succeeded: Prodigal [2024-01-24 10:47:36,433] [INFO] Task started: HMMsearch [2024-01-24 10:47:36,433] [INFO] Running command: hmmsearch --tblout GCF_026410085.1_ASM2641008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/reference_markers.hmm GCF_026410085.1_ASM2641008v1_genomic.fna/protein.faa > /dev/null [2024-01-24 10:47:36,834] [INFO] Task succeeded: HMMsearch [2024-01-24 10:47:36,835] [INFO] Found 6/6 markers. [2024-01-24 10:47:36,883] [INFO] Query marker FASTA was written to GCF_026410085.1_ASM2641008v1_genomic.fna/markers.fasta [2024-01-24 10:47:36,884] [INFO] Task started: Blastn [2024-01-24 10:47:36,884] [INFO] Running command: blastn -query GCF_026410085.1_ASM2641008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/reference_markers.fasta -out GCF_026410085.1_ASM2641008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 10:47:37,931] [INFO] Task succeeded: Blastn [2024-01-24 10:47:37,934] [INFO] Selected 21 target genomes. [2024-01-24 10:47:37,934] [INFO] Target genome list was writen to GCF_026410085.1_ASM2641008v1_genomic.fna/target_genomes.txt [2024-01-24 10:47:38,555] [INFO] Task started: fastANI [2024-01-24 10:47:38,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgd19f7981-76a1-476b-81d1-fdaddb89e026/GCF_026410085.1_ASM2641008v1_genomic.fna.gz --refList GCF_026410085.1_ASM2641008v1_genomic.fna/target_genomes.txt --output GCF_026410085.1_ASM2641008v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 10:48:10,580] [INFO] Task succeeded: fastANI [2024-01-24 10:48:10,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 10:48:10,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 10:48:10,600] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold) [2024-01-24 10:48:10,600] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 10:48:10,601] [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 marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.3051 1549 1875 95 below_threshold Pseudomonas lactucae strain=MAFF 301380 GCA_016937615.1 2813360 2813360 type True 87.8223 1393 1875 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 87.66 1534 1875 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.6241 1528 1875 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 87.5961 1525 1875 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.4382 1507 1875 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 87.3319 1541 1875 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 87.3099 1532 1875 95 below_threshold Pseudomonas tolaasii strain=NCPPB 2192 GCA_002813445.1 29442 29442 type True 87.0467 1472 1875 95 below_threshold Pseudomonas tolaasii GCA_900625075.1 29442 29442 type True 87.0455 1454 1875 95 below_threshold Pseudomonas tolaasii strain=CCUG 23369 GCA_008801395.1 29442 29442 type True 87.0175 1456 1875 95 below_threshold Pseudomonas libanensis strain=DSM 17149 GCA_001439685.1 75588 75588 type True 86.8511 1482 1875 95 below_threshold Pseudomonas synxantha strain=LMG 2190 GCA_900105675.1 47883 47883 type True 86.8455 1498 1875 95 below_threshold Pseudomonas synxantha strain=NCTC10696 GCA_901482615.1 47883 47883 type True 86.8395 1511 1875 95 below_threshold Pseudomonas synxantha strain=DSM 18928 GCA_001439725.1 47883 47883 type True 86.7908 1499 1875 95 below_threshold Pseudomonas synxantha strain=NBRC 3913 GCA_002091795.1 47883 47883 type True 86.7681 1499 1875 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 86.7196 1494 1875 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 86.7089 1404 1875 95 below_threshold Pseudomonas edaphica strain=RD25 GCA_005863185.1 2006980 2006980 type True 86.6699 1145 1875 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.3538 1359 1875 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.6563 1222 1875 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 10:48:10,602] [INFO] DFAST Taxonomy check result was written to GCF_026410085.1_ASM2641008v1_genomic.fna/tc_result.tsv [2024-01-24 10:48:10,605] [INFO] ===== Taxonomy check completed ===== [2024-01-24 10:48:10,606] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 10:48:10,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/checkm_data [2024-01-24 10:48:10,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 10:48:10,665] [INFO] Task started: CheckM [2024-01-24 10:48:10,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026410085.1_ASM2641008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026410085.1_ASM2641008v1_genomic.fna/checkm_input GCF_026410085.1_ASM2641008v1_genomic.fna/checkm_result [2024-01-24 10:49:17,517] [INFO] Task succeeded: CheckM [2024-01-24 10:49:17,518] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 10:49:17,545] [INFO] ===== Completeness check finished ===== [2024-01-24 10:49:17,546] [INFO] ===== Start GTDB Search ===== [2024-01-24 10:49:17,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026410085.1_ASM2641008v1_genomic.fna/markers.fasta) [2024-01-24 10:49:17,547] [INFO] Task started: Blastn [2024-01-24 10:49:17,547] [INFO] Running command: blastn -query GCF_026410085.1_ASM2641008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d5f144-4379-483d-afcd-cdaa061257c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_026410085.1_ASM2641008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 10:49:19,292] [INFO] Task succeeded: Blastn [2024-01-24 10:49:19,297] [INFO] Selected 18 target genomes. [2024-01-24 10:49:19,297] [INFO] Target genome list was writen to GCF_026410085.1_ASM2641008v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 10:49:19,310] [INFO] Task started: fastANI [2024-01-24 10:49:19,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgd19f7981-76a1-476b-81d1-fdaddb89e026/GCF_026410085.1_ASM2641008v1_genomic.fna.gz --refList GCF_026410085.1_ASM2641008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026410085.1_ASM2641008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 10:49:47,876] [INFO] Task succeeded: fastANI [2024-01-24 10:49:47,891] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 10:49:47,891] [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_013522705.1 s__Pseudomonas_E sp002383725 99.0708 1755 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.07 99.06 0.96 0.95 3 conclusive GCF_007858255.1 s__Pseudomonas_E rhodesiae 91.1143 1609 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.21 97.47 0.91 0.84 28 - GCF_900105325.1 s__Pseudomonas_E marginalis 88.2668 1584 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.53 96.47 0.90 0.85 19 - GCF_007858185.1 s__Pseudomonas_E grimontii 88.1275 1529 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCF_014207255.1 s__Pseudomonas_E sp014207255 88.1062 1561 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.31 98.90 0.95 0.91 5 - GCF_002843605.1 s__Pseudomonas_E sp002843605 87.8046 1539 1875 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_003612935.1 s__Pseudomonas_E sp003013355 87.7708 1558 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.87 98.56 0.95 0.92 7 - GCF_015163715.1 s__Pseudomonas_E cyclaminis 87.6094 1381 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.88 95.83 0.83 0.80 14 - GCF_002007785.1 s__Pseudomonas_E azotoformans_B 87.5769 1560 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.95 98.86 0.94 0.92 6 - GCF_001439695.1 s__Pseudomonas_E veronii 87.5622 1449 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.79 98.13 0.89 0.82 43 - GCF_013385985.1 s__Pseudomonas_E sp013385985 87.3795 1469 1875 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_013386585.1 s__Pseudomonas_E sp013386585 87.3792 1448 1875 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_900111895.1 s__Pseudomonas_E simiae 87.3067 1534 1875 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_001439815.1 s__Pseudomonas_E orientalis 87.0762 1468 1875 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_002813445.1 s__Pseudomonas_E tolaasii 87.0672 1470 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.61 99.17 0.97 0.93 14 - GCF_003852315.1 s__Pseudomonas_E sp003014915 87.0619 1522 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.48 96.20 0.95 0.91 10 - GCF_900105675.1 s__Pseudomonas_E synxantha 86.8484 1497 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.7053 98.15 96.46 0.93 0.84 14 - GCF_003851495.1 s__Pseudomonas_E fluorescens_BB 86.7924 1489 1875 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.3929 98.85 97.70 0.94 0.89 3 - -------------------------------------------------------------------------------- [2024-01-24 10:49:47,893] [INFO] GTDB search result was written to GCF_026410085.1_ASM2641008v1_genomic.fna/result_gtdb.tsv [2024-01-24 10:49:47,894] [INFO] ===== GTDB Search completed ===== [2024-01-24 10:49:47,898] [INFO] DFAST_QC result json was written to GCF_026410085.1_ASM2641008v1_genomic.fna/dqc_result.json [2024-01-24 10:49:47,898] [INFO] DFAST_QC completed! [2024-01-24 10:49:47,898] [INFO] Total running time: 0h2m41s