[2024-01-24 14:55:20,965] [INFO] DFAST_QC pipeline started. [2024-01-24 14:55:20,968] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:55:20,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference [2024-01-24 14:55:22,175] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:55:22,176] [INFO] Task started: Prodigal [2024-01-24 14:55:22,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dd62ec0-c4f2-44ff-86ed-3bafa0583e03/GCF_013392005.1_ASM1339200v1_genomic.fna.gz | prodigal -d GCF_013392005.1_ASM1339200v1_genomic.fna/cds.fna -a GCF_013392005.1_ASM1339200v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:55:42,405] [INFO] Task succeeded: Prodigal [2024-01-24 14:55:42,406] [INFO] Task started: HMMsearch [2024-01-24 14:55:42,406] [INFO] Running command: hmmsearch --tblout GCF_013392005.1_ASM1339200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/reference_markers.hmm GCF_013392005.1_ASM1339200v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:55:42,777] [INFO] Task succeeded: HMMsearch [2024-01-24 14:55:42,778] [INFO] Found 6/6 markers. [2024-01-24 14:55:42,839] [INFO] Query marker FASTA was written to GCF_013392005.1_ASM1339200v1_genomic.fna/markers.fasta [2024-01-24 14:55:42,839] [INFO] Task started: Blastn [2024-01-24 14:55:42,839] [INFO] Running command: blastn -query GCF_013392005.1_ASM1339200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/reference_markers.fasta -out GCF_013392005.1_ASM1339200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:55:43,923] [INFO] Task succeeded: Blastn [2024-01-24 14:55:43,926] [INFO] Selected 18 target genomes. [2024-01-24 14:55:43,926] [INFO] Target genome list was writen to GCF_013392005.1_ASM1339200v1_genomic.fna/target_genomes.txt [2024-01-24 14:55:43,935] [INFO] Task started: fastANI [2024-01-24 14:55:43,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd62ec0-c4f2-44ff-86ed-3bafa0583e03/GCF_013392005.1_ASM1339200v1_genomic.fna.gz --refList GCF_013392005.1_ASM1339200v1_genomic.fna/target_genomes.txt --output GCF_013392005.1_ASM1339200v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:56:11,734] [INFO] Task succeeded: fastANI [2024-01-24 14:56:11,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:56:11,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:56:11,750] [INFO] Found 18 fastANI hits (5 hits with ANI > threshold) [2024-01-24 14:56:11,751] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:56:11,751] [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 azotoformans GCA_900624915.1 47878 47878 suspected-type True 95.9701 1751 2015 95 conclusive Pseudomonas azotoformans strain=DSM 18862 GCA_001983205.1 47878 47878 suspected-type True 95.9324 1757 2015 95 conclusive Pseudomonas azotoformans strain=LMG 21611 GCA_001870415.1 47878 47878 suspected-type True 95.9256 1756 2015 95 conclusive Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 95.9113 1747 2015 95 conclusive Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 95.9024 1761 2015 95 conclusive Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 94.7449 1655 2015 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 94.7391 1664 2015 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 94.7189 1664 2015 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 90.9682 1645 2015 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 90.2002 1573 2015 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 89.197 1565 2015 95 below_threshold Pseudomonas cedrina subsp. cedrina GCA_900625035.1 76762 651740 type True 89.0053 1502 2015 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.8752 1348 2015 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.095 1209 2015 95 below_threshold Pseudomonas jessenii strain=DSM 17150 GCA_002236115.1 77298 77298 suspected-type True 83.662 1102 2015 95 below_threshold Pseudomonas azerbaijanoccidens strain=SWRI74 GCA_019145495.1 2842347 2842347 type True 83.3291 1112 2015 95 below_threshold Pseudomonas iranensis strain=SWRI54 GCA_014268585.2 2745503 2745503 type True 83.2899 1102 2015 95 below_threshold Pseudomonas atacamensis strain=M7D1 GCA_004801935.1 2565368 2565368 type True 83.2557 1104 2015 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:56:11,752] [INFO] DFAST Taxonomy check result was written to GCF_013392005.1_ASM1339200v1_genomic.fna/tc_result.tsv [2024-01-24 14:56:11,753] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:56:11,753] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:56:11,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/checkm_data [2024-01-24 14:56:11,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:56:11,817] [INFO] Task started: CheckM [2024-01-24 14:56:11,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013392005.1_ASM1339200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013392005.1_ASM1339200v1_genomic.fna/checkm_input GCF_013392005.1_ASM1339200v1_genomic.fna/checkm_result [2024-01-24 14:57:11,145] [INFO] Task succeeded: CheckM [2024-01-24 14:57:11,146] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:57:11,165] [INFO] ===== Completeness check finished ===== [2024-01-24 14:57:11,165] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:57:11,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013392005.1_ASM1339200v1_genomic.fna/markers.fasta) [2024-01-24 14:57:11,166] [INFO] Task started: Blastn [2024-01-24 14:57:11,166] [INFO] Running command: blastn -query GCF_013392005.1_ASM1339200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4425e6d5-c83a-410d-9f2b-a701c3cc06e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013392005.1_ASM1339200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:57:12,989] [INFO] Task succeeded: Blastn [2024-01-24 14:57:12,993] [INFO] Selected 20 target genomes. [2024-01-24 14:57:12,993] [INFO] Target genome list was writen to GCF_013392005.1_ASM1339200v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:57:13,011] [INFO] Task started: fastANI [2024-01-24 14:57:13,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd62ec0-c4f2-44ff-86ed-3bafa0583e03/GCF_013392005.1_ASM1339200v1_genomic.fna.gz --refList GCF_013392005.1_ASM1339200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013392005.1_ASM1339200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:57:42,361] [INFO] Task succeeded: fastANI [2024-01-24 14:57:42,377] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:57:42,377] [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_900103345.1 s__Pseudomonas_E azotoformans 95.9003 1762 2015 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.97 95.87 0.94 0.87 9 conclusive GCF_001870465.1 s__Pseudomonas_E extremorientalis 94.7189 1664 2015 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 91.056 1616 2015 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_000612585.1 s__Pseudomonas_E sp000612585 91.0176 1500 2015 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_000503215.1 s__Pseudomonas_E canadensis 90.5683 1573 2015 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.83 97.74 0.94 0.91 12 - GCF_001579805.1 s__Pseudomonas_E azotoformans_A 90.4916 1622 2015 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_013385825.1 s__Pseudomonas_E reactans 90.4484 1570 2015 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_001645105.1 s__Pseudomonas_E marginalis_B 90.4067 1565 2015 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_002563895.1 s__Pseudomonas_E lurida 90.2026 1572 2015 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_900111895.1 s__Pseudomonas_E simiae 90.1966 1553 2015 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_001186335.1 s__Pseudomonas_E trivialis_B 89.8103 1545 2015 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_002843605.1 s__Pseudomonas_E sp002843605 89.1916 1539 2015 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_012844475.1 s__Pseudomonas_E sp012844475 89.0999 1368 2015 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_013386585.1 s__Pseudomonas_E sp013386585 89.0885 1486 2015 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_001983175.1 s__Pseudomonas_E cedrina 89.0339 1498 2015 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_900107155.1 s__Pseudomonas_E salomonii 88.8257 1598 2015 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_001439695.1 s__Pseudomonas_E veronii 88.2998 1449 2015 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_900215245.1 s__Pseudomonas_E fluorescens 87.8476 1488 2015 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.68 99.25 0.98 0.92 14 - GCF_001439815.1 s__Pseudomonas_E orientalis 87.6941 1422 2015 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_001439845.1 s__Pseudomonas_E lactis 87.5341 1449 2015 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.24 95.50 0.88 0.81 30 - -------------------------------------------------------------------------------- [2024-01-24 14:57:42,379] [INFO] GTDB search result was written to GCF_013392005.1_ASM1339200v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:57:42,380] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:57:42,385] [INFO] DFAST_QC result json was written to GCF_013392005.1_ASM1339200v1_genomic.fna/dqc_result.json [2024-01-24 14:57:42,385] [INFO] DFAST_QC completed! [2024-01-24 14:57:42,385] [INFO] Total running time: 0h2m21s