[2024-01-25 19:12:20,905] [INFO] DFAST_QC pipeline started. [2024-01-25 19:12:20,907] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:12:20,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference [2024-01-25 19:12:22,042] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:12:22,042] [INFO] Task started: Prodigal [2024-01-25 19:12:22,043] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcef7799-ffe5-49bf-811d-79f5b43edf94/GCF_020097395.1_ASM2009739v1_genomic.fna.gz | prodigal -d GCF_020097395.1_ASM2009739v1_genomic.fna/cds.fna -a GCF_020097395.1_ASM2009739v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:12:34,543] [INFO] Task succeeded: Prodigal [2024-01-25 19:12:34,543] [INFO] Task started: HMMsearch [2024-01-25 19:12:34,544] [INFO] Running command: hmmsearch --tblout GCF_020097395.1_ASM2009739v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/reference_markers.hmm GCF_020097395.1_ASM2009739v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:12:34,843] [INFO] Task succeeded: HMMsearch [2024-01-25 19:12:34,844] [INFO] Found 6/6 markers. [2024-01-25 19:12:34,888] [INFO] Query marker FASTA was written to GCF_020097395.1_ASM2009739v1_genomic.fna/markers.fasta [2024-01-25 19:12:34,888] [INFO] Task started: Blastn [2024-01-25 19:12:34,888] [INFO] Running command: blastn -query GCF_020097395.1_ASM2009739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/reference_markers.fasta -out GCF_020097395.1_ASM2009739v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:12:35,721] [INFO] Task succeeded: Blastn [2024-01-25 19:12:35,724] [INFO] Selected 22 target genomes. [2024-01-25 19:12:35,724] [INFO] Target genome list was writen to GCF_020097395.1_ASM2009739v1_genomic.fna/target_genomes.txt [2024-01-25 19:12:35,745] [INFO] Task started: fastANI [2024-01-25 19:12:35,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcef7799-ffe5-49bf-811d-79f5b43edf94/GCF_020097395.1_ASM2009739v1_genomic.fna.gz --refList GCF_020097395.1_ASM2009739v1_genomic.fna/target_genomes.txt --output GCF_020097395.1_ASM2009739v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:12:58,710] [INFO] Task succeeded: fastANI [2024-01-25 19:12:58,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:12:58,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:12:58,722] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold) [2024-01-25 19:12:58,723] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:12:58,723] [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 Leclercia adecarboxylata strain=FDAARGOS_1505 GCA_020097395.1 83655 83655 suspected-type True 100.0 1685 1685 95 conclusive Leclercia adecarboxylata strain=NBRC 102595 GCA_001515505.1 83655 83655 suspected-type True 99.9641 1621 1685 95 conclusive Leclercia adecarboxylata strain=ATCC 23216 GCA_000735515.1 83655 83655 suspected-type True 99.9448 1592 1685 95 conclusive Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 84.4012 1087 1685 95 below_threshold Enterobacter chengduensis strain=WCHECl-C4 = WCHECh050004 GCA_001984825.2 2494701 2494701 type True 84.372 1122 1685 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 84.349 1103 1685 95 below_threshold Leclercia pneumoniae strain=49125 GCA_018987305.1 2815358 2815358 type True 84.3349 1141 1685 95 below_threshold Leclercia pneumoniae strain=49125 GCA_017348915.1 2815358 2815358 type True 84.3305 1169 1685 95 below_threshold Enterobacter roggenkampii strain=FDAARGOS 1430 GCA_019047025.1 1812935 1812935 type True 84.3027 1134 1685 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 84.2938 1125 1685 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 84.2897 1137 1685 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 84.1827 1125 1685 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 84.0459 1064 1685 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 84.0067 1084 1685 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_002939185.1 2071710 2071710 type True 83.9878 1060 1685 95 below_threshold Enterobacter kobei strain=DSM 13645 GCA_001729765.1 208224 208224 type True 83.9699 1075 1685 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 83.9657 1125 1685 95 below_threshold Shewanella khirikhana strain=TH2012 GCA_003957745.1 1965282 1965282 type True 77.6025 91 1685 95 below_threshold Oceanimonas marisflavi strain=102-Na3 GCA_003049725.1 2059724 2059724 type True 76.7617 89 1685 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:12:58,725] [INFO] DFAST Taxonomy check result was written to GCF_020097395.1_ASM2009739v1_genomic.fna/tc_result.tsv [2024-01-25 19:12:58,725] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:12:58,725] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:12:58,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/checkm_data [2024-01-25 19:12:58,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:12:58,774] [INFO] Task started: CheckM [2024-01-25 19:12:58,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097395.1_ASM2009739v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097395.1_ASM2009739v1_genomic.fna/checkm_input GCF_020097395.1_ASM2009739v1_genomic.fna/checkm_result [2024-01-25 19:13:37,964] [INFO] Task succeeded: CheckM [2024-01-25 19:13:37,965] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:13:37,986] [INFO] ===== Completeness check finished ===== [2024-01-25 19:13:37,986] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:13:37,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097395.1_ASM2009739v1_genomic.fna/markers.fasta) [2024-01-25 19:13:37,987] [INFO] Task started: Blastn [2024-01-25 19:13:37,987] [INFO] Running command: blastn -query GCF_020097395.1_ASM2009739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c40e084-2d67-4f3f-85c5-ff38d400c7fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097395.1_ASM2009739v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:13:39,184] [INFO] Task succeeded: Blastn [2024-01-25 19:13:39,187] [INFO] Selected 12 target genomes. [2024-01-25 19:13:39,188] [INFO] Target genome list was writen to GCF_020097395.1_ASM2009739v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:13:39,203] [INFO] Task started: fastANI [2024-01-25 19:13:39,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcef7799-ffe5-49bf-811d-79f5b43edf94/GCF_020097395.1_ASM2009739v1_genomic.fna.gz --refList GCF_020097395.1_ASM2009739v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097395.1_ASM2009739v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:13:55,041] [INFO] Task succeeded: fastANI [2024-01-25 19:13:55,049] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:13:55,049] [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 GCA_901472455.1 s__Leclercia adecarboxylata 99.7877 1683 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.53 98.09 0.95 0.87 86 conclusive GCF_006874705.1 s__Leclercia adecarboxylata_C 91.7729 1386 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.71 98.25 0.93 0.90 13 - GCF_011290365.1 s__Leclercia sp003024485 91.6713 1391 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.06 98.06 0.90 0.90 2 - GCA_002360945.1 s__Leclercia adecarboxylata_B 91.5206 1344 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 99.97 99.97 0.98 0.98 2 - GCF_006171285.1 s__Leclercia adecarboxylata_A 89.5843 1387 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 97.80 96.55 0.92 0.89 4 - GCF_002902985.1 s__Leclercia sp002902985 89.0786 1362 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.13 96.37 0.93 0.86 16 - GCF_013927005.1 s__Enterobacter sp013927005 84.0555 1138 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_018323985.1 s__Enterobacter_D kobei_A 82.3733 985 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D 95.0 99.37 98.44 0.98 0.93 6 - GCF_000735365.1 s__Kluyvera ascorbata 82.214 876 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 98.94 97.70 0.94 0.89 5 - GCF_002915575.1 s__Superficieibacter electus 81.105 828 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter 95.0 99.98 99.98 1.00 1.00 2 - GCF_014155765.1 s__Pantoea dispersa 79.4674 575 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea 95.0 97.93 96.36 0.92 0.86 38 - GCA_002386445.1 s__Pseudomonas_E sp002386445 79.0456 92 1685 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 19:13:55,051] [INFO] GTDB search result was written to GCF_020097395.1_ASM2009739v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:13:55,051] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:13:55,054] [INFO] DFAST_QC result json was written to GCF_020097395.1_ASM2009739v1_genomic.fna/dqc_result.json [2024-01-25 19:13:55,054] [INFO] DFAST_QC completed! [2024-01-25 19:13:55,054] [INFO] Total running time: 0h1m34s