[2024-01-24 13:19:00,958] [INFO] DFAST_QC pipeline started. [2024-01-24 13:19:00,961] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:19:00,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference [2024-01-24 13:19:02,303] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:19:02,304] [INFO] Task started: Prodigal [2024-01-24 13:19:02,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg9246b6f8-46d8-41c4-a086-8af7d02b3f76/GCF_007858255.1_ASM785825v1_genomic.fna.gz | prodigal -d GCF_007858255.1_ASM785825v1_genomic.fna/cds.fna -a GCF_007858255.1_ASM785825v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:19:24,822] [INFO] Task succeeded: Prodigal [2024-01-24 13:19:24,822] [INFO] Task started: HMMsearch [2024-01-24 13:19:24,823] [INFO] Running command: hmmsearch --tblout GCF_007858255.1_ASM785825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/reference_markers.hmm GCF_007858255.1_ASM785825v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:19:25,190] [INFO] Task succeeded: HMMsearch [2024-01-24 13:19:25,192] [INFO] Found 6/6 markers. [2024-01-24 13:19:25,254] [INFO] Query marker FASTA was written to GCF_007858255.1_ASM785825v1_genomic.fna/markers.fasta [2024-01-24 13:19:25,255] [INFO] Task started: Blastn [2024-01-24 13:19:25,255] [INFO] Running command: blastn -query GCF_007858255.1_ASM785825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/reference_markers.fasta -out GCF_007858255.1_ASM785825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:19:26,262] [INFO] Task succeeded: Blastn [2024-01-24 13:19:26,266] [INFO] Selected 33 target genomes. [2024-01-24 13:19:26,267] [INFO] Target genome list was writen to GCF_007858255.1_ASM785825v1_genomic.fna/target_genomes.txt [2024-01-24 13:19:26,288] [INFO] Task started: fastANI [2024-01-24 13:19:26,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg9246b6f8-46d8-41c4-a086-8af7d02b3f76/GCF_007858255.1_ASM785825v1_genomic.fna.gz --refList GCF_007858255.1_ASM785825v1_genomic.fna/target_genomes.txt --output GCF_007858255.1_ASM785825v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:20:10,048] [INFO] Task succeeded: fastANI [2024-01-24 13:20:10,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:20:10,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:20:10,072] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold) [2024-01-24 13:20:10,072] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 13:20:10,072] [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 88.0257 1578 2070 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 87.5427 1561 2070 95 below_threshold Pseudomonas asgharzadehiana strain=SWRI132 GCA_019139815.1 2842349 2842349 type True 87.518 1532 2070 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 87.4946 1545 2070 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 87.4918 1542 2070 95 below_threshold Pseudomonas lactucae strain=MAFF 301380 GCA_016937615.1 2813360 2813360 type True 87.4294 1436 2070 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 87.4248 1545 2070 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.3265 1547 2070 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.3079 1528 2070 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 87.2418 1538 2070 95 below_threshold Pseudomonas kairouanensis strain=KC12 GCA_004682055.1 2293832 2293832 type True 87.194 1476 2070 95 below_threshold Pseudomonas nabeulensis strain=E10B GCA_004682045.1 2293833 2293833 type True 87.0873 1461 2070 95 below_threshold Pseudomonas tolaasii strain=NCPPB 2192 GCA_002813445.1 29442 29442 type True 86.8657 1460 2070 95 below_threshold Pseudomonas tolaasii GCA_900625075.1 29442 29442 type True 86.8641 1454 2070 95 below_threshold Pseudomonas tolaasii strain=CCUG 23369 GCA_008801395.1 29442 29442 type True 86.844 1460 2070 95 below_threshold Pseudomonas cremoris strain=WS 5106 GCA_014230465.1 2724178 2724178 type True 86.8358 1489 2070 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 86.7509 1493 2070 95 below_threshold Pseudomonas synxantha strain=DSM 18928 GCA_001439725.1 47883 47883 type True 86.7178 1510 2070 95 below_threshold Pseudomonas synxantha strain=NBRC 3913 GCA_002091795.1 47883 47883 type True 86.6925 1520 2070 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 86.6892 1487 2070 95 below_threshold Pseudomonas synxantha strain=LMG 2190 GCA_900105675.1 47883 47883 type True 86.6801 1525 2070 95 below_threshold Pseudomonas synxantha strain=NCTC10696 GCA_901482615.1 47883 47883 type True 86.6626 1527 2070 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 86.6489 1512 2070 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 86.5664 1402 2070 95 below_threshold Pseudomonas palleroniana strain=CCUG 51524 GCA_008801495.1 191390 191390 type True 86.5156 1470 2070 95 below_threshold Pseudomonas palleroniana strain=LMG 23076 GCA_003031675.1 191390 191390 type True 86.497 1448 2070 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 86.4785 1497 2070 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.2819 1365 2070 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.6393 1247 2070 95 below_threshold Lysobacter prati strain=SYSU H10001 GCA_009765215.1 2596704 2596704 type True 76.4682 93 2070 95 below_threshold Lysobacter arenosi strain=R7 GCA_016613475.2 2795387 2795387 type True 76.1113 123 2070 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:20:10,074] [INFO] DFAST Taxonomy check result was written to GCF_007858255.1_ASM785825v1_genomic.fna/tc_result.tsv [2024-01-24 13:20:10,074] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:20:10,074] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:20:10,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/checkm_data [2024-01-24 13:20:10,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:20:10,135] [INFO] Task started: CheckM [2024-01-24 13:20:10,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007858255.1_ASM785825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007858255.1_ASM785825v1_genomic.fna/checkm_input GCF_007858255.1_ASM785825v1_genomic.fna/checkm_result [2024-01-24 13:21:12,941] [INFO] Task succeeded: CheckM [2024-01-24 13:21:12,942] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:21:12,965] [INFO] ===== Completeness check finished ===== [2024-01-24 13:21:12,966] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:21:12,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007858255.1_ASM785825v1_genomic.fna/markers.fasta) [2024-01-24 13:21:12,967] [INFO] Task started: Blastn [2024-01-24 13:21:12,967] [INFO] Running command: blastn -query GCF_007858255.1_ASM785825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c5e20d7-0f48-4b2f-a4f2-110f221593f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_007858255.1_ASM785825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:21:14,313] [INFO] Task succeeded: Blastn [2024-01-24 13:21:14,317] [INFO] Selected 26 target genomes. [2024-01-24 13:21:14,318] [INFO] Target genome list was writen to GCF_007858255.1_ASM785825v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:21:14,343] [INFO] Task started: fastANI [2024-01-24 13:21:14,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg9246b6f8-46d8-41c4-a086-8af7d02b3f76/GCF_007858255.1_ASM785825v1_genomic.fna.gz --refList GCF_007858255.1_ASM785825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007858255.1_ASM785825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:21:51,700] [INFO] Task succeeded: fastANI [2024-01-24 13:21:51,724] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:21:51,724] [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_007858255.1 s__Pseudomonas_E rhodesiae 100.0 2064 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.21 97.47 0.91 0.84 28 conclusive GCF_013522705.1 s__Pseudomonas_E sp002383725 91.0808 1618 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.07 99.06 0.96 0.95 3 - GCF_900105325.1 s__Pseudomonas_E marginalis 87.9365 1609 2070 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_002843605.1 s__Pseudomonas_E sp002843605 87.6978 1526 2070 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 87.5755 1569 2070 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_009866765.1 s__Pseudomonas_E sp009866765 87.5031 1520 2070 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_001870465.1 s__Pseudomonas_E extremorientalis 87.4763 1547 2070 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 87.4614 1550 2070 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_002007785.1 s__Pseudomonas_E azotoformans_B 87.4494 1526 2070 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_013386585.1 s__Pseudomonas_E sp013386585 87.3863 1454 2070 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_001439695.1 s__Pseudomonas_E veronii 87.3593 1528 2070 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_002563895.1 s__Pseudomonas_E lurida 87.317 1526 2070 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_001050345.1 s__Pseudomonas_E fildesensis 87.2961 1539 2070 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_013385985.1 s__Pseudomonas_E sp013385985 87.1676 1504 2070 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_012844475.1 s__Pseudomonas_E sp012844475 86.9922 1454 2070 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_002813445.1 s__Pseudomonas_E tolaasii 86.878 1458 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.61 99.17 0.97 0.93 14 - GCA_016937595.1 s__Pseudomonas_E fulgida 86.8766 1039 2070 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_002837185.1 s__Pseudomonas_E fluorescens_AM 86.8349 1456 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.23 99.16 0.96 0.94 7 - GCF_002934065.1 s__Pseudomonas_E orientalis_A 86.7076 1469 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.15 95.96 0.86 0.83 21 - GCF_900105675.1 s__Pseudomonas_E synxantha 86.6808 1525 2070 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 86.5454 1484 2070 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_003031675.1 s__Pseudomonas_E palleroniana 86.4871 1450 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.85 97.94 0.95 0.90 8 - GCF_002287825.1 s__Pseudomonas_E koreensis_B 83.0936 1256 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.58 96.55 0.92 0.86 13 - GCF_900105155.1 s__Pseudomonas_E prosekii 82.8289 1194 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.41 96.34 0.92 0.89 8 - GCF_002269125.1 s__Pseudomonas_E lundensis_A 80.9699 827 2070 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.91 98.32 0.91 0.90 4 - GCF_004803755.1 s__Pseudomonas_E sp004803755 80.2204 817 2070 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 13:21:51,726] [INFO] GTDB search result was written to GCF_007858255.1_ASM785825v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:21:51,726] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:21:51,731] [INFO] DFAST_QC result json was written to GCF_007858255.1_ASM785825v1_genomic.fna/dqc_result.json [2024-01-24 13:21:51,731] [INFO] DFAST_QC completed! [2024-01-24 13:21:51,732] [INFO] Total running time: 0h2m51s