[2024-01-24 10:57:38,757] [INFO] DFAST_QC pipeline started. [2024-01-24 10:57:38,759] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 10:57:38,759] [INFO] DQC Reference Directory: /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference [2024-01-24 10:57:40,173] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 10:57:40,173] [INFO] Task started: Prodigal [2024-01-24 10:57:40,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg938a6aa0-c14a-414c-8176-d4657a828a1e/GCF_024169765.1_ASM2416976v1_genomic.fna.gz | prodigal -d GCF_024169765.1_ASM2416976v1_genomic.fna/cds.fna -a GCF_024169765.1_ASM2416976v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 10:57:59,534] [INFO] Task succeeded: Prodigal [2024-01-24 10:57:59,535] [INFO] Task started: HMMsearch [2024-01-24 10:57:59,535] [INFO] Running command: hmmsearch --tblout GCF_024169765.1_ASM2416976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/reference_markers.hmm GCF_024169765.1_ASM2416976v1_genomic.fna/protein.faa > /dev/null [2024-01-24 10:57:59,861] [INFO] Task succeeded: HMMsearch [2024-01-24 10:57:59,862] [INFO] Found 6/6 markers. [2024-01-24 10:57:59,912] [INFO] Query marker FASTA was written to GCF_024169765.1_ASM2416976v1_genomic.fna/markers.fasta [2024-01-24 10:57:59,912] [INFO] Task started: Blastn [2024-01-24 10:57:59,912] [INFO] Running command: blastn -query GCF_024169765.1_ASM2416976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/reference_markers.fasta -out GCF_024169765.1_ASM2416976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 10:58:00,894] [INFO] Task succeeded: Blastn [2024-01-24 10:58:00,898] [INFO] Selected 25 target genomes. [2024-01-24 10:58:00,898] [INFO] Target genome list was writen to GCF_024169765.1_ASM2416976v1_genomic.fna/target_genomes.txt [2024-01-24 10:58:00,926] [INFO] Task started: fastANI [2024-01-24 10:58:00,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg938a6aa0-c14a-414c-8176-d4657a828a1e/GCF_024169765.1_ASM2416976v1_genomic.fna.gz --refList GCF_024169765.1_ASM2416976v1_genomic.fna/target_genomes.txt --output GCF_024169765.1_ASM2416976v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 10:58:34,545] [INFO] Task succeeded: fastANI [2024-01-24 10:58:34,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 10:58:34,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 10:58:34,563] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold) [2024-01-24 10:58:34,564] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 10:58:34,564] [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 88.2724 1526 1907 95 below_threshold Pseudomonas lactucae strain=MAFF 301380 GCA_016937615.1 2813360 2813360 type True 87.7902 1391 1907 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 87.6608 1545 1907 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 87.6328 1548 1907 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.6086 1529 1907 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.3705 1507 1907 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 87.3404 1526 1907 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 87.3135 1536 1907 95 below_threshold Pseudomonas tolaasii GCA_900625075.1 29442 29442 type True 87.1252 1424 1907 95 below_threshold Pseudomonas tolaasii strain=NCPPB 2192 GCA_002813445.1 29442 29442 type True 87.1067 1452 1907 95 below_threshold Pseudomonas tolaasii strain=CCUG 23369 GCA_008801395.1 29442 29442 type True 87.0831 1423 1907 95 below_threshold Pseudomonas synxantha strain=NCTC10696 GCA_901482615.1 47883 47883 type True 86.8417 1497 1907 95 below_threshold Pseudomonas synxantha strain=LMG 2190 GCA_900105675.1 47883 47883 type True 86.8021 1500 1907 95 below_threshold Pseudomonas synxantha strain=NBRC 3913 GCA_002091795.1 47883 47883 type True 86.7816 1480 1907 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 86.765 1488 1907 95 below_threshold Pseudomonas synxantha strain=DSM 18928 GCA_001439725.1 47883 47883 type True 86.7583 1495 1907 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 86.7487 1421 1907 95 below_threshold Pseudomonas palleroniana strain=LMG 23076 GCA_003031675.1 191390 191390 type True 86.6512 1456 1907 95 below_threshold Pseudomonas edaphica strain=RD25 GCA_005863185.1 2006980 2006980 type True 86.6277 1144 1907 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.3253 1359 1907 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.6203 1243 1907 95 below_threshold Pseudomonas taetrolens strain=NCTC10697 GCA_900475285.1 47884 47884 type True 81.2157 859 1907 95 below_threshold Pseudomonas taetrolens strain=DSM 21104 GCA_001042915.1 47884 47884 type True 81.09 861 1907 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 10:58:34,566] [INFO] DFAST Taxonomy check result was written to GCF_024169765.1_ASM2416976v1_genomic.fna/tc_result.tsv [2024-01-24 10:58:34,568] [INFO] ===== Taxonomy check completed ===== [2024-01-24 10:58:34,568] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 10:58:34,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/checkm_data [2024-01-24 10:58:34,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 10:58:34,627] [INFO] Task started: CheckM [2024-01-24 10:58:34,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024169765.1_ASM2416976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024169765.1_ASM2416976v1_genomic.fna/checkm_input GCF_024169765.1_ASM2416976v1_genomic.fna/checkm_result [2024-01-24 10:59:30,518] [INFO] Task succeeded: CheckM [2024-01-24 10:59:30,520] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 10:59:30,543] [INFO] ===== Completeness check finished ===== [2024-01-24 10:59:30,543] [INFO] ===== Start GTDB Search ===== [2024-01-24 10:59:30,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024169765.1_ASM2416976v1_genomic.fna/markers.fasta) [2024-01-24 10:59:30,544] [INFO] Task started: Blastn [2024-01-24 10:59:30,544] [INFO] Running command: blastn -query GCF_024169765.1_ASM2416976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf37a0306-9c3a-416c-bc7f-72fe5c1aad17/dqc_reference/reference_markers_gtdb.fasta -out GCF_024169765.1_ASM2416976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 10:59:32,196] [INFO] Task succeeded: Blastn [2024-01-24 10:59:32,201] [INFO] Selected 22 target genomes. [2024-01-24 10:59:32,202] [INFO] Target genome list was writen to GCF_024169765.1_ASM2416976v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 10:59:32,218] [INFO] Task started: fastANI [2024-01-24 10:59:32,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg938a6aa0-c14a-414c-8176-d4657a828a1e/GCF_024169765.1_ASM2416976v1_genomic.fna.gz --refList GCF_024169765.1_ASM2416976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024169765.1_ASM2416976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:00:02,766] [INFO] Task succeeded: fastANI [2024-01-24 11:00:02,787] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:00:02,787] [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 99.1852 1753 1907 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 91.152 1612 1907 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 88.2493 1564 1907 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 88.1662 1526 1907 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 88.1405 1559 1907 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 87.8447 1524 1907 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 87.775 1538 1907 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 87.5753 1398 1907 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 87.5302 1542 1907 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 87.498 1469 1907 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 87.3939 1460 1907 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 87.3738 1441 1907 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 87.3218 1535 1907 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_002813445.1 s__Pseudomonas_E tolaasii 87.0938 1454 1907 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 87.0671 1521 1907 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 86.7925 1501 1907 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 86.7636 1484 1907 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_004519405.1 s__Pseudomonas_E sp004519405 86.4842 1489 1907 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_001874645.1 s__Pseudomonas_E frederiksbergensis_B 83.0626 1084 1907 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_900475285.1 s__Pseudomonas_E taetrolens 81.1937 859 1907 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.99 99.98 0.99 0.99 4 - -------------------------------------------------------------------------------- [2024-01-24 11:00:02,789] [INFO] GTDB search result was written to GCF_024169765.1_ASM2416976v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:00:02,789] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:00:02,793] [INFO] DFAST_QC result json was written to GCF_024169765.1_ASM2416976v1_genomic.fna/dqc_result.json [2024-01-24 11:00:02,794] [INFO] DFAST_QC completed! [2024-01-24 11:00:02,794] [INFO] Total running time: 0h2m24s