[2024-01-24 13:55:15,155] [INFO] DFAST_QC pipeline started. [2024-01-24 13:55:15,157] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:55:15,157] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference [2024-01-24 13:55:16,485] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:55:16,486] [INFO] Task started: Prodigal [2024-01-24 13:55:16,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9189e09-b12b-4c79-8e1a-6724b1ca64a5/GCF_021166635.1_ASM2116663v1_genomic.fna.gz | prodigal -d GCF_021166635.1_ASM2116663v1_genomic.fna/cds.fna -a GCF_021166635.1_ASM2116663v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:55:40,002] [INFO] Task succeeded: Prodigal [2024-01-24 13:55:40,002] [INFO] Task started: HMMsearch [2024-01-24 13:55:40,003] [INFO] Running command: hmmsearch --tblout GCF_021166635.1_ASM2116663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/reference_markers.hmm GCF_021166635.1_ASM2116663v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:55:40,408] [INFO] Task succeeded: HMMsearch [2024-01-24 13:55:40,409] [INFO] Found 6/6 markers. [2024-01-24 13:55:40,475] [INFO] Query marker FASTA was written to GCF_021166635.1_ASM2116663v1_genomic.fna/markers.fasta [2024-01-24 13:55:40,476] [INFO] Task started: Blastn [2024-01-24 13:55:40,476] [INFO] Running command: blastn -query GCF_021166635.1_ASM2116663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/reference_markers.fasta -out GCF_021166635.1_ASM2116663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:55:41,493] [INFO] Task succeeded: Blastn [2024-01-24 13:55:41,497] [INFO] Selected 16 target genomes. [2024-01-24 13:55:41,497] [INFO] Target genome list was writen to GCF_021166635.1_ASM2116663v1_genomic.fna/target_genomes.txt [2024-01-24 13:55:41,511] [INFO] Task started: fastANI [2024-01-24 13:55:41,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9189e09-b12b-4c79-8e1a-6724b1ca64a5/GCF_021166635.1_ASM2116663v1_genomic.fna.gz --refList GCF_021166635.1_ASM2116663v1_genomic.fna/target_genomes.txt --output GCF_021166635.1_ASM2116663v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:56:06,331] [INFO] Task succeeded: fastANI [2024-01-24 13:56:06,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:56:06,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:56:06,345] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:56:06,345] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:56:06,346] [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=ICMP 3553 GCA_001645105.1 298 298 suspected-type True 98.7945 1872 2155 95 conclusive Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 98.7285 1775 2155 95 conclusive Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 91.1759 1631 2155 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 90.974 1615 2155 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 90.4971 1586 2155 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 90.4763 1635 2155 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 90.4375 1651 2155 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 90.4288 1635 2155 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 90.2999 1574 2155 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 90.2832 1568 2155 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 89.4267 1687 2155 95 below_threshold Pseudomonas asgharzadehiana strain=SWRI132 GCA_019139815.1 2842349 2842349 type True 88.3497 1541 2155 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 88.0283 1478 2155 95 below_threshold Pseudomonas salmasensis strain=SWRI126 GCA_014268375.2 2745514 2745514 type True 87.6746 1484 2155 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.8492 1405 2155 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.1728 1254 2155 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:56:06,347] [INFO] DFAST Taxonomy check result was written to GCF_021166635.1_ASM2116663v1_genomic.fna/tc_result.tsv [2024-01-24 13:56:06,348] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:56:06,348] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:56:06,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/checkm_data [2024-01-24 13:56:06,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:56:06,418] [INFO] Task started: CheckM [2024-01-24 13:56:06,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021166635.1_ASM2116663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021166635.1_ASM2116663v1_genomic.fna/checkm_input GCF_021166635.1_ASM2116663v1_genomic.fna/checkm_result [2024-01-24 13:57:16,019] [INFO] Task succeeded: CheckM [2024-01-24 13:57:16,020] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:57:16,042] [INFO] ===== Completeness check finished ===== [2024-01-24 13:57:16,043] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:57:16,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021166635.1_ASM2116663v1_genomic.fna/markers.fasta) [2024-01-24 13:57:16,044] [INFO] Task started: Blastn [2024-01-24 13:57:16,044] [INFO] Running command: blastn -query GCF_021166635.1_ASM2116663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7aa8fae-3532-4f88-be3c-75d2e74c0db5/dqc_reference/reference_markers_gtdb.fasta -out GCF_021166635.1_ASM2116663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:57:17,685] [INFO] Task succeeded: Blastn [2024-01-24 13:57:17,689] [INFO] Selected 19 target genomes. [2024-01-24 13:57:17,690] [INFO] Target genome list was writen to GCF_021166635.1_ASM2116663v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:57:17,709] [INFO] Task started: fastANI [2024-01-24 13:57:17,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9189e09-b12b-4c79-8e1a-6724b1ca64a5/GCF_021166635.1_ASM2116663v1_genomic.fna.gz --refList GCF_021166635.1_ASM2116663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021166635.1_ASM2116663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:57:47,704] [INFO] Task succeeded: fastANI [2024-01-24 13:57:47,721] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:57:47,722] [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_001645105.1 s__Pseudomonas_E marginalis_B 98.7945 1872 2155 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 conclusive GCF_000612585.1 s__Pseudomonas_E sp000612585 91.3858 1531 2155 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_002007785.1 s__Pseudomonas_E azotoformans_B 91.1206 1628 2155 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_002563895.1 s__Pseudomonas_E lurida 90.9761 1615 2155 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_900103345.1 s__Pseudomonas_E azotoformans 90.4933 1633 2155 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_001870465.1 s__Pseudomonas_E extremorientalis 90.4107 1594 2155 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_001579805.1 s__Pseudomonas_E azotoformans_A 90.3427 1627 2155 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_001186335.1 s__Pseudomonas_E trivialis_B 90.3083 1636 2155 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_900111895.1 s__Pseudomonas_E simiae 90.2832 1568 2155 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 89.4713 1572 2155 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_014207255.1 s__Pseudomonas_E sp014207255 89.4292 1660 2155 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_012844475.1 s__Pseudomonas_E sp012844475 89.2891 1449 2155 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 88.9475 1073 2155 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_001050345.1 s__Pseudomonas_E fildesensis 88.7533 1570 2155 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 88.6087 1526 2155 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_009834565.1 s__Pseudomonas_E sp009834565 88.5864 1551 2155 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.71 97.35 0.93 0.93 3 - GCF_001439695.1 s__Pseudomonas_E veronii 88.4448 1514 2155 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_900583165.1 s__Pseudomonas_E sp900583165 88.1657 1455 2155 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.99 99.99 1.00 0.99 4 - GCF_001902145.1 s__Pseudomonas_E fluorescens_BV 87.6482 1440 2155 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.76 95.23 0.87 0.84 22 - -------------------------------------------------------------------------------- [2024-01-24 13:57:47,723] [INFO] GTDB search result was written to GCF_021166635.1_ASM2116663v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:57:47,724] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:57:47,728] [INFO] DFAST_QC result json was written to GCF_021166635.1_ASM2116663v1_genomic.fna/dqc_result.json [2024-01-24 13:57:47,729] [INFO] DFAST_QC completed! [2024-01-24 13:57:47,729] [INFO] Total running time: 0h2m33s