[2024-01-24 11:44:22,866] [INFO] DFAST_QC pipeline started. [2024-01-24 11:44:22,868] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:44:22,869] [INFO] DQC Reference Directory: /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference [2024-01-24 11:44:26,345] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:44:26,346] [INFO] Task started: Prodigal [2024-01-24 11:44:26,346] [INFO] Running command: gunzip -c /var/lib/cwl/stga6407f99-c68b-4f4c-87f5-87ae1526cc34/GCF_004331265.1_ASM433126v1_genomic.fna.gz | prodigal -d GCF_004331265.1_ASM433126v1_genomic.fna/cds.fna -a GCF_004331265.1_ASM433126v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:44:39,949] [INFO] Task succeeded: Prodigal [2024-01-24 11:44:39,950] [INFO] Task started: HMMsearch [2024-01-24 11:44:39,951] [INFO] Running command: hmmsearch --tblout GCF_004331265.1_ASM433126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/reference_markers.hmm GCF_004331265.1_ASM433126v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:44:40,243] [INFO] Task succeeded: HMMsearch [2024-01-24 11:44:40,245] [INFO] Found 6/6 markers. [2024-01-24 11:44:40,289] [INFO] Query marker FASTA was written to GCF_004331265.1_ASM433126v1_genomic.fna/markers.fasta [2024-01-24 11:44:40,290] [INFO] Task started: Blastn [2024-01-24 11:44:40,290] [INFO] Running command: blastn -query GCF_004331265.1_ASM433126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/reference_markers.fasta -out GCF_004331265.1_ASM433126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:44:41,255] [INFO] Task succeeded: Blastn [2024-01-24 11:44:41,258] [INFO] Selected 18 target genomes. [2024-01-24 11:44:41,259] [INFO] Target genome list was writen to GCF_004331265.1_ASM433126v1_genomic.fna/target_genomes.txt [2024-01-24 11:44:41,267] [INFO] Task started: fastANI [2024-01-24 11:44:41,267] [INFO] Running command: fastANI --query /var/lib/cwl/stga6407f99-c68b-4f4c-87f5-87ae1526cc34/GCF_004331265.1_ASM433126v1_genomic.fna.gz --refList GCF_004331265.1_ASM433126v1_genomic.fna/target_genomes.txt --output GCF_004331265.1_ASM433126v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:45:02,918] [INFO] Task succeeded: fastANI [2024-01-24 11:45:02,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:45:02,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:45:02,937] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold) [2024-01-24 11:45:02,937] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:45:02,937] [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 Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 100.0 1612 1615 95 conclusive Enterobacter quasimori strain=090044 GCA_003964905.1 2838947 2838947 type True 90.1089 1288 1615 95 below_threshold Enterobacter mori strain=LMG 25706 GCA_000211415.1 539813 539813 type True 89.9996 1282 1615 95 below_threshold Enterobacter asburiae strain=ATCC 35953 GCA_001521715.1 61645 61645 type True 89.7063 1230 1615 95 below_threshold Enterobacter asburiae strain=FDAARGOS_892 GCA_016027695.1 61645 61645 type True 89.6445 1235 1615 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 89.2093 1289 1615 95 below_threshold Enterobacter chengduensis strain=WCHECl-C4 = WCHECh050004 GCA_001984825.2 2494701 2494701 type True 89.1511 1249 1615 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 89.0962 1293 1615 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 89.0414 1202 1615 95 below_threshold Enterobacter roggenkampii strain=FDAARGOS 1430 GCA_019047025.1 1812935 1812935 type True 89.0343 1272 1615 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_001729805.1 1812935 1812935 type True 88.9974 1285 1615 95 below_threshold Enterobacter vonholyi strain=E13 GCA_008364555.1 2797505 2797505 type True 88.9147 1238 1615 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 88.357 1226 1615 95 below_threshold Enterobacter hormaechei subsp. oharae strain=FDAARGOS_1533 GCA_020097195.1 301102 158836 type True 88.3449 1286 1615 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 88.2784 1271 1615 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 87.9027 1289 1615 95 below_threshold Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 87.5962 1260 1615 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 87.5809 1265 1615 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:45:02,939] [INFO] DFAST Taxonomy check result was written to GCF_004331265.1_ASM433126v1_genomic.fna/tc_result.tsv [2024-01-24 11:45:02,939] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:45:02,940] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:45:02,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/checkm_data [2024-01-24 11:45:02,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:45:02,986] [INFO] Task started: CheckM [2024-01-24 11:45:02,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331265.1_ASM433126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331265.1_ASM433126v1_genomic.fna/checkm_input GCF_004331265.1_ASM433126v1_genomic.fna/checkm_result [2024-01-24 11:45:44,504] [INFO] Task succeeded: CheckM [2024-01-24 11:45:44,505] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:45:44,523] [INFO] ===== Completeness check finished ===== [2024-01-24 11:45:44,524] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:45:44,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331265.1_ASM433126v1_genomic.fna/markers.fasta) [2024-01-24 11:45:44,524] [INFO] Task started: Blastn [2024-01-24 11:45:44,525] [INFO] Running command: blastn -query GCF_004331265.1_ASM433126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde904524-9f9f-4004-86ac-b6ac08eb9919/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331265.1_ASM433126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:45:46,077] [INFO] Task succeeded: Blastn [2024-01-24 11:45:46,086] [INFO] Selected 15 target genomes. [2024-01-24 11:45:46,087] [INFO] Target genome list was writen to GCF_004331265.1_ASM433126v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:45:46,113] [INFO] Task started: fastANI [2024-01-24 11:45:46,114] [INFO] Running command: fastANI --query /var/lib/cwl/stga6407f99-c68b-4f4c-87f5-87ae1526cc34/GCF_004331265.1_ASM433126v1_genomic.fna.gz --refList GCF_004331265.1_ASM433126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331265.1_ASM433126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:46:03,745] [INFO] Task succeeded: fastANI [2024-01-24 11:46:03,765] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:46:03,766] [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_004331265.1 s__Enterobacter wuhouensis 100.0 1612 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 conclusive GCF_003594935.1 s__Enterobacter huaxiensis 90.8046 1363 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.98 98.98 0.94 0.94 2 - GCF_000211415.1 s__Enterobacter mori 89.9957 1282 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.59 96.13 0.88 0.85 23 - GCF_003634515.1 s__Enterobacter asburiae_A 89.9924 1298 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.0274 97.62 96.46 0.91 0.85 7 - GCF_001521715.1 s__Enterobacter asburiae 89.6961 1231 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.42 96.92 0.89 0.84 32 - GCF_007035645.1 s__Enterobacter asburiae_B 89.6374 1249 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.31 97.34 0.92 0.85 70 - GCF_000493015.1 s__Enterobacter sp000493015 89.6358 1284 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.7595 98.68 98.68 0.92 0.92 2 - GCF_009755685.1 s__Enterobacter sp000568095 89.3657 1251 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0476 98.37 98.04 0.95 0.92 11 - GCF_003594915.1 s__Enterobacter chuandaensis 89.2984 1253 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 98.32 0.92 0.92 3 - GCF_900324475.1 s__Enterobacter bugandensis 89.2157 1289 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.49 95.52 0.94 0.88 115 - GCF_011754535.1 s__Enterobacter cloacae_N 89.1888 1275 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.03 98.99 0.93 0.91 4 - GCF_001984825.2 s__Enterobacter chengduensis 89.1394 1250 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.11 95.58 0.88 0.79 24 - GCF_008364555.1 s__Enterobacter vonholyi 88.9147 1238 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.34 98.09 0.94 0.93 8 - GCF_004402045.1 s__Enterobacter nimipressuralis_A 88.7766 1275 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_013375935.1 s__Enterobacter cloacae_O 88.2489 1304 1615 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.68 98.59 0.94 0.92 6 - -------------------------------------------------------------------------------- [2024-01-24 11:46:03,768] [INFO] GTDB search result was written to GCF_004331265.1_ASM433126v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:46:03,768] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:46:03,773] [INFO] DFAST_QC result json was written to GCF_004331265.1_ASM433126v1_genomic.fna/dqc_result.json [2024-01-24 11:46:03,774] [INFO] DFAST_QC completed! [2024-01-24 11:46:03,774] [INFO] Total running time: 0h1m41s