[2023-06-27 01:24:10,004] [INFO] DFAST_QC pipeline started. [2023-06-27 01:24:10,085] [INFO] DFAST_QC version: 0.5.7 [2023-06-27 01:24:10,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference [2023-06-27 01:24:11,315] [INFO] ===== Start taxonomy check using ANI ===== [2023-06-27 01:24:11,316] [INFO] Task started: Prodigal [2023-06-27 01:24:11,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ad24c8-f6c3-43d1-89f3-39e678c5c079/GCA_002341985.1_ASM234198v1_genomic.fna.gz | prodigal -d GCA_002341985.1_ASM234198v1_genomic.fna/cds.fna -a GCA_002341985.1_ASM234198v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2023-06-27 01:24:23,259] [INFO] Task succeeded: Prodigal [2023-06-27 01:24:23,260] [INFO] Task started: HMMsearch [2023-06-27 01:24:23,260] [INFO] Running command: hmmsearch --tblout GCA_002341985.1_ASM234198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/reference_markers.hmm GCA_002341985.1_ASM234198v1_genomic.fna/protein.faa > /dev/null [2023-06-27 01:24:23,561] [INFO] Task succeeded: HMMsearch [2023-06-27 01:24:23,563] [INFO] Found 6/6 markers. [2023-06-27 01:24:23,605] [INFO] Query marker FASTA was written to GCA_002341985.1_ASM234198v1_genomic.fna/markers.fasta [2023-06-27 01:24:23,605] [INFO] Task started: Blastn [2023-06-27 01:24:23,606] [INFO] Running command: blastn -query GCA_002341985.1_ASM234198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/reference_markers.fasta -out GCA_002341985.1_ASM234198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-27 01:24:24,520] [INFO] Task succeeded: Blastn [2023-06-27 01:24:24,525] [INFO] Selected 15 target genomes. [2023-06-27 01:24:24,526] [INFO] Target genome list was writen to GCA_002341985.1_ASM234198v1_genomic.fna/target_genomes.txt [2023-06-27 01:24:24,531] [INFO] Task started: fastANI [2023-06-27 01:24:24,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ad24c8-f6c3-43d1-89f3-39e678c5c079/GCA_002341985.1_ASM234198v1_genomic.fna.gz --refList GCA_002341985.1_ASM234198v1_genomic.fna/target_genomes.txt --output GCA_002341985.1_ASM234198v1_genomic.fna/fastani_result.tsv --threads 1 [2023-06-27 01:24:39,896] [INFO] Task succeeded: fastANI [2023-06-27 01:24:39,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2023-06-27 01:24:39,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2023-06-27 01:24:39,918] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold) [2023-06-27 01:24:39,918] [INFO] The taxonomy check result is classified as 'conclusive'. [2023-06-27 01:24:39,918] [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 pneumoniae strain=49125 GCA_017348915.1 2815358 2815358 type True 98.5982 1344 1440 95 conclusive Leclercia pneumoniae strain=49125 GCA_018987305.1 2815358 2815358 type True 98.5916 1341 1440 95 conclusive Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 84.7594 1049 1440 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 84.6388 1056 1440 95 below_threshold Leclercia adecarboxylata strain=ATCC 23216 GCA_000735515.1 83655 83655 suspected-type True 84.312 1102 1440 95 below_threshold Leclercia adecarboxylata strain=FDAARGOS_1505 GCA_020097395.1 83655 83655 suspected-type True 84.2831 1135 1440 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 84.2806 1076 1440 95 below_threshold Leclercia adecarboxylata strain=NBRC 102595 GCA_001515505.1 83655 83655 suspected-type True 84.2675 1116 1440 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 84.233 1017 1440 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 84.1166 1054 1440 95 below_threshold Enterobacter oligotrophicus strain=CCA6 GCA_009176645.1 2478464 2478464 type True 84.1021 1048 1440 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 84.1012 1068 1440 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 83.9599 1036 1440 95 below_threshold Enterobacter hormaechei subsp. steigerwaltii strain=DSM 16691 GCA_001729725.1 299766 158836 type True 83.912 1072 1440 95 below_threshold Enterobacter hormaechei subsp. hoffmannii strain=DSM 14563 GCA_001729745.1 1812934 158836 type True 83.8722 1054 1440 95 below_threshold -------------------------------------------------------------------------------- [2023-06-27 01:24:39,920] [INFO] DFAST Taxonomy check result was written to GCA_002341985.1_ASM234198v1_genomic.fna/tc_result.tsv [2023-06-27 01:24:39,921] [INFO] ===== Taxonomy check completed ===== [2023-06-27 01:24:39,921] [INFO] ===== Start completeness check using CheckM ===== [2023-06-27 01:24:39,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/checkm_data [2023-06-27 01:24:39,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2023-06-27 01:24:39,970] [INFO] Task started: CheckM [2023-06-27 01:24:39,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002341985.1_ASM234198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002341985.1_ASM234198v1_genomic.fna/checkm_input GCA_002341985.1_ASM234198v1_genomic.fna/checkm_result [2023-06-27 01:25:18,968] [INFO] Task succeeded: CheckM [2023-06-27 01:25:18,970] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 79.17% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2023-06-27 01:25:18,992] [INFO] ===== Completeness check finished ===== [2023-06-27 01:25:18,993] [INFO] ===== Start GTDB Search ===== [2023-06-27 01:25:18,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002341985.1_ASM234198v1_genomic.fna/markers.fasta) [2023-06-27 01:25:18,994] [INFO] Task started: Blastn [2023-06-27 01:25:18,994] [INFO] Running command: blastn -query GCA_002341985.1_ASM234198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f928da-cb38-4d0d-9505-84167ab76edf/dqc_reference/reference_markers_gtdb.fasta -out GCA_002341985.1_ASM234198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-27 01:25:20,438] [INFO] Task succeeded: Blastn [2023-06-27 01:25:20,444] [INFO] Selected 18 target genomes. [2023-06-27 01:25:20,444] [INFO] Target genome list was writen to GCA_002341985.1_ASM234198v1_genomic.fna/target_genomes_gtdb.txt [2023-06-27 01:25:20,456] [INFO] Task started: fastANI [2023-06-27 01:25:20,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ad24c8-f6c3-43d1-89f3-39e678c5c079/GCA_002341985.1_ASM234198v1_genomic.fna.gz --refList GCA_002341985.1_ASM234198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002341985.1_ASM234198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2023-06-27 01:25:41,621] [INFO] Task succeeded: fastANI [2023-06-27 01:25:41,649] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius) [2023-06-27 01:25:41,649] [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_017348915.1 s__UBA7405 sp000755535 98.5982 1344 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405 95.0 98.56 97.85 0.93 0.89 10 conclusive GCA_002469605.1 s__UBA7405 sp002469605 85.5498 793 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405 95.0 N/A N/A N/A N/A 1 - GCF_019047785.1 s__Enterobacter cancerogenus 84.7446 1051 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.78 98.42 0.93 0.90 16 - GCF_006171285.1 s__Leclercia adecarboxylata_A 84.5743 1111 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 97.80 96.55 0.92 0.89 4 - GCF_011290365.1 s__Leclercia sp003024485 84.529 1111 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.06 98.06 0.90 0.90 2 - GCF_006874705.1 s__Leclercia adecarboxylata_C 84.514 1112 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.71 98.25 0.93 0.90 13 - GCA_002360945.1 s__Leclercia adecarboxylata_B 84.4252 1123 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 99.97 99.97 0.98 0.98 2 - GCF_004331265.1 s__Enterobacter wuhouensis 84.2862 1075 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_003594915.1 s__Enterobacter chuandaensis 84.1859 1029 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 98.32 0.92 0.92 3 - GCF_007035645.1 s__Enterobacter asburiae_B 84.1814 1037 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.31 97.34 0.92 0.85 70 - GCF_008364625.1 s__Enterobacter dykesii 84.1706 1019 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.5795 99.13 97.97 0.97 0.95 7 - GCA_901472455.1 s__Leclercia adecarboxylata 84.1241 1116 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.53 98.09 0.95 0.87 86 - GCF_003594935.1 s__Enterobacter huaxiensis 84.1087 1064 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.98 98.98 0.94 0.94 2 - GCF_009176645.1 s__Enterobacter oligotrophicus 84.1003 1048 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.55 99.09 0.97 0.94 3 - GCF_000211415.1 s__Enterobacter mori 84.0837 1052 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.59 96.13 0.88 0.85 23 - GCF_011754535.1 s__Enterobacter cloacae_N 84.0769 1043 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.03 98.99 0.93 0.91 4 - GCF_001729745.1 s__Enterobacter hormaechei_A 83.8567 1056 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 96.63 95.22 0.89 0.83 1867 - GCF_003057745.1 s__Enterobacter sp003057745 83.8549 997 1440 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2023-06-27 01:25:41,651] [INFO] GTDB search result was written to GCA_002341985.1_ASM234198v1_genomic.fna/result_gtdb.tsv [2023-06-27 01:25:41,652] [INFO] ===== GTDB Search completed ===== [2023-06-27 01:25:41,656] [INFO] DFAST_QC result json was written to GCA_002341985.1_ASM234198v1_genomic.fna/dqc_result.json [2023-06-27 01:25:41,656] [INFO] DFAST_QC completed! [2023-06-27 01:25:41,657] [INFO] Total running time: 0h1m32s