[2024-01-24 13:17:33,528] [INFO] DFAST_QC pipeline started. [2024-01-24 13:17:33,530] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:17:33,531] [INFO] DQC Reference Directory: /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference [2024-01-24 13:17:34,957] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:17:34,958] [INFO] Task started: Prodigal [2024-01-24 13:17:34,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg93375ee0-f11c-4b59-9276-062ad8c00284/GCF_004682045.1_ASM468204v1_genomic.fna.gz | prodigal -d GCF_004682045.1_ASM468204v1_genomic.fna/cds.fna -a GCF_004682045.1_ASM468204v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:18:00,533] [INFO] Task succeeded: Prodigal [2024-01-24 13:18:00,533] [INFO] Task started: HMMsearch [2024-01-24 13:18:00,533] [INFO] Running command: hmmsearch --tblout GCF_004682045.1_ASM468204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/reference_markers.hmm GCF_004682045.1_ASM468204v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:18:00,897] [INFO] Task succeeded: HMMsearch [2024-01-24 13:18:00,899] [INFO] Found 6/6 markers. [2024-01-24 13:18:00,956] [INFO] Query marker FASTA was written to GCF_004682045.1_ASM468204v1_genomic.fna/markers.fasta [2024-01-24 13:18:00,956] [INFO] Task started: Blastn [2024-01-24 13:18:00,957] [INFO] Running command: blastn -query GCF_004682045.1_ASM468204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/reference_markers.fasta -out GCF_004682045.1_ASM468204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:18:01,829] [INFO] Task succeeded: Blastn [2024-01-24 13:18:01,833] [INFO] Selected 25 target genomes. [2024-01-24 13:18:01,833] [INFO] Target genome list was writen to GCF_004682045.1_ASM468204v1_genomic.fna/target_genomes.txt [2024-01-24 13:18:01,843] [INFO] Task started: fastANI [2024-01-24 13:18:01,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg93375ee0-f11c-4b59-9276-062ad8c00284/GCF_004682045.1_ASM468204v1_genomic.fna.gz --refList GCF_004682045.1_ASM468204v1_genomic.fna/target_genomes.txt --output GCF_004682045.1_ASM468204v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:18:39,708] [INFO] Task succeeded: fastANI [2024-01-24 13:18:39,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:18:39,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:18:39,735] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:18:39,735] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:18:39,735] [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 nabeulensis strain=E10B GCA_004682045.1 2293833 2293833 type True 100.0 2169 2177 95 conclusive Pseudomonas cremoris strain=WS 5106 GCA_014230465.1 2724178 2724178 type True 89.9828 1653 2177 95 below_threshold Pseudomonas kairouanensis strain=KC12 GCA_004682055.1 2293832 2293832 type True 89.8806 1712 2177 95 below_threshold Pseudomonas pisciculturae strain=P115 GCA_015461805.1 2730413 2730413 type True 89.3336 1630 2177 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_001870415.1 47878 47878 suspected-type True 89.0275 1614 2177 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 88.9822 1606 2177 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 88.9239 1641 2177 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 88.9174 1635 2177 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 88.8315 1575 2177 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 88.8109 1584 2177 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 88.7985 1610 2177 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 88.7568 1586 2177 95 below_threshold Pseudomonas canadensis strain=2-92 GCA_000503215.1 915099 915099 type True 88.7518 1584 2177 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.6568 1579 2177 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 88.5383 1577 2177 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 88.2734 1611 2177 95 below_threshold Pseudomonas salomonii strain=LMG 22120 GCA_001730645.1 191391 191391 type True 88.0469 1532 2177 95 below_threshold Pseudomonas salomonii strain=ICMP 14252 GCA_900107155.1 191391 191391 type True 88.0293 1548 2177 95 below_threshold Pseudomonas tolaasii strain=CCUG 23369 GCA_008801395.1 29442 29442 type True 87.9678 1544 2177 95 below_threshold Pseudomonas tolaasii GCA_900625075.1 29442 29442 type True 87.9352 1542 2177 95 below_threshold Pseudomonas edaphica strain=RD25 GCA_005863185.1 2006980 2006980 type True 87.9093 1189 2177 95 below_threshold Pseudomonas tolaasii strain=NCPPB 2192 GCA_002813445.1 29442 29442 type True 87.9013 1552 2177 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.904 1399 2177 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.1763 1266 2177 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:18:39,737] [INFO] DFAST Taxonomy check result was written to GCF_004682045.1_ASM468204v1_genomic.fna/tc_result.tsv [2024-01-24 13:18:39,737] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:18:39,737] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:18:39,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/checkm_data [2024-01-24 13:18:39,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:18:39,807] [INFO] Task started: CheckM [2024-01-24 13:18:39,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004682045.1_ASM468204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004682045.1_ASM468204v1_genomic.fna/checkm_input GCF_004682045.1_ASM468204v1_genomic.fna/checkm_result [2024-01-24 13:19:53,153] [INFO] Task succeeded: CheckM [2024-01-24 13:19:53,155] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:19:53,173] [INFO] ===== Completeness check finished ===== [2024-01-24 13:19:53,174] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:19:53,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004682045.1_ASM468204v1_genomic.fna/markers.fasta) [2024-01-24 13:19:53,175] [INFO] Task started: Blastn [2024-01-24 13:19:53,175] [INFO] Running command: blastn -query GCF_004682045.1_ASM468204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4b0df23-a094-4a7b-afdd-a4e990cf095d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004682045.1_ASM468204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:19:54,535] [INFO] Task succeeded: Blastn [2024-01-24 13:19:54,540] [INFO] Selected 25 target genomes. [2024-01-24 13:19:54,540] [INFO] Target genome list was writen to GCF_004682045.1_ASM468204v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:19:54,565] [INFO] Task started: fastANI [2024-01-24 13:19:54,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg93375ee0-f11c-4b59-9276-062ad8c00284/GCF_004682045.1_ASM468204v1_genomic.fna.gz --refList GCF_004682045.1_ASM468204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004682045.1_ASM468204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:20:33,813] [INFO] Task succeeded: fastANI [2024-01-24 13:20:33,839] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:20:33,839] [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_004682045.1 s__Pseudomonas_E nabeulensis 100.0 2169 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.61 95.59 0.85 0.85 3 conclusive GCF_014230465.1 s__Pseudomonas_E cremoris 89.9728 1656 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.87 96.78 0.87 0.83 4 - GCF_004682055.1 s__Pseudomonas_E kairouanensis 89.8819 1712 2177 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_000346755.1 s__Pseudomonas_E sp000346755 89.3524 1527 2177 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_015461805.1 s__Pseudomonas_E pisciculturae 89.3321 1631 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.09 99.09 0.95 0.95 2 - GCF_003852405.1 s__Pseudomonas_E sp003852405 89.2114 1608 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.89 95.89 0.88 0.88 2 - GCF_014851685.1 s__Pseudomonas_E sp014851685 88.9562 1532 2177 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_001579805.1 s__Pseudomonas_E azotoformans_A 88.9561 1640 2177 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_900103345.1 s__Pseudomonas_E azotoformans 88.9276 1634 2177 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_000612585.1 s__Pseudomonas_E sp000612585 88.8897 1541 2177 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_013385825.1 s__Pseudomonas_E reactans 88.8669 1612 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.45 96.30 0.89 0.87 7 - GCF_001870465.1 s__Pseudomonas_E extremorientalis 88.839 1574 2177 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_002007785.1 s__Pseudomonas_E azotoformans_B 88.8097 1622 2177 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_013385985.1 s__Pseudomonas_E sp013385985 88.794 1591 2177 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 88.7529 1570 2177 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_002979555.1 s__Pseudomonas_E sp002979555 88.6442 1489 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.44 99.31 0.96 0.95 11 - GCF_001186335.1 s__Pseudomonas_E trivialis_B 88.6062 1591 2177 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_900105325.1 s__Pseudomonas_E marginalis 88.6003 1623 2177 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_003612935.1 s__Pseudomonas_E sp003013355 88.3731 1655 2177 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_002563895.1 s__Pseudomonas_E lurida 88.256 1613 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.19 99.03 0.94 0.91 25 - GCF_900107155.1 s__Pseudomonas_E salomonii 88.0192 1549 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.30 96.43 0.92 0.87 14 - GCF_001983175.1 s__Pseudomonas_E cedrina 87.9865 1533 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 - GCF_002813445.1 s__Pseudomonas_E tolaasii 87.8898 1553 2177 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_004519405.1 s__Pseudomonas_E sp004519405 87.3437 1495 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.60 98.40 0.98 0.92 5 - GCF_018614775.1 s__Pseudomonas_E fluorescens_BY 83.3144 1048 2177 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:20:33,841] [INFO] GTDB search result was written to GCF_004682045.1_ASM468204v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:20:33,841] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:20:33,846] [INFO] DFAST_QC result json was written to GCF_004682045.1_ASM468204v1_genomic.fna/dqc_result.json [2024-01-24 13:20:33,846] [INFO] DFAST_QC completed! [2024-01-24 13:20:33,846] [INFO] Total running time: 0h3m0s