[2024-01-24 14:03:08,311] [INFO] DFAST_QC pipeline started. [2024-01-24 14:03:08,314] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:03:08,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference [2024-01-24 14:03:09,662] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:03:09,663] [INFO] Task started: Prodigal [2024-01-24 14:03:09,663] [INFO] Running command: gunzip -c /var/lib/cwl/stga2afd9cc-364d-4de8-a211-8b891571b568/GCF_021172065.1_ASM2117206v1_genomic.fna.gz | prodigal -d GCF_021172065.1_ASM2117206v1_genomic.fna/cds.fna -a GCF_021172065.1_ASM2117206v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:03:23,536] [INFO] Task succeeded: Prodigal [2024-01-24 14:03:23,536] [INFO] Task started: HMMsearch [2024-01-24 14:03:23,536] [INFO] Running command: hmmsearch --tblout GCF_021172065.1_ASM2117206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/reference_markers.hmm GCF_021172065.1_ASM2117206v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:03:23,890] [INFO] Task succeeded: HMMsearch [2024-01-24 14:03:23,892] [INFO] Found 6/6 markers. [2024-01-24 14:03:23,958] [INFO] Query marker FASTA was written to GCF_021172065.1_ASM2117206v1_genomic.fna/markers.fasta [2024-01-24 14:03:23,959] [INFO] Task started: Blastn [2024-01-24 14:03:23,959] [INFO] Running command: blastn -query GCF_021172065.1_ASM2117206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/reference_markers.fasta -out GCF_021172065.1_ASM2117206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:03:25,021] [INFO] Task succeeded: Blastn [2024-01-24 14:03:25,024] [INFO] Selected 15 target genomes. [2024-01-24 14:03:25,024] [INFO] Target genome list was writen to GCF_021172065.1_ASM2117206v1_genomic.fna/target_genomes.txt [2024-01-24 14:03:25,029] [INFO] Task started: fastANI [2024-01-24 14:03:25,029] [INFO] Running command: fastANI --query /var/lib/cwl/stga2afd9cc-364d-4de8-a211-8b891571b568/GCF_021172065.1_ASM2117206v1_genomic.fna.gz --refList GCF_021172065.1_ASM2117206v1_genomic.fna/target_genomes.txt --output GCF_021172065.1_ASM2117206v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:03:43,611] [INFO] Task succeeded: fastANI [2024-01-24 14:03:43,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:03:43,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:03:43,628] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold) [2024-01-24 14:03:43,629] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:03:43,629] [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 Pseudocitrobacter corydidari GCA_021172065.1 2891570 2891570 type True 100.0 1671 1671 95 conclusive Pseudocitrobacter vendiensis strain=type strain: CPO20170097 GCA_943590815.1 2488306 2488306 type True 93.5281 1365 1671 95 below_threshold Kluyvera sichuanensis strain=090646 GCA_014218705.1 2725494 2725494 type True 83.2009 1030 1671 95 below_threshold Kluyvera georgiana strain=ATCC 51603 GCA_001654985.1 73098 73098 type True 83.0338 1000 1671 95 below_threshold Kluyvera ascorbata strain=ATCC 33433 GCA_000735365.1 51288 51288 suspected-type True 82.9041 991 1671 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 82.2935 935 1671 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 82.2459 886 1671 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 82.2261 936 1671 95 below_threshold Escherichia fergusonii strain=FDAARGOS_1499 GCA_020097475.1 564 564 type True 82.0814 789 1671 95 below_threshold Enterobacter cloacae strain=ATCC 13047 GCA_000755525.1 550 550 type True 82.038 914 1671 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_013376815.1 550 550 type True 82.0016 931 1671 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 81.9919 946 1671 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 81.9459 922 1671 95 below_threshold Citrobacter rodentium strain=DSM 16636 GCA_021278985.1 67825 67825 type True 81.7847 931 1671 95 below_threshold Raoultella terrigena strain=NBRC 14941 GCA_006539725.1 577 577 type True 81.6627 927 1671 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:03:43,631] [INFO] DFAST Taxonomy check result was written to GCF_021172065.1_ASM2117206v1_genomic.fna/tc_result.tsv [2024-01-24 14:03:43,631] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:03:43,631] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:03:43,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/checkm_data [2024-01-24 14:03:43,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:03:43,681] [INFO] Task started: CheckM [2024-01-24 14:03:43,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021172065.1_ASM2117206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021172065.1_ASM2117206v1_genomic.fna/checkm_input GCF_021172065.1_ASM2117206v1_genomic.fna/checkm_result [2024-01-24 14:04:27,510] [INFO] Task succeeded: CheckM [2024-01-24 14:04:27,511] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:04:27,531] [INFO] ===== Completeness check finished ===== [2024-01-24 14:04:27,532] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:04:27,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021172065.1_ASM2117206v1_genomic.fna/markers.fasta) [2024-01-24 14:04:27,532] [INFO] Task started: Blastn [2024-01-24 14:04:27,533] [INFO] Running command: blastn -query GCF_021172065.1_ASM2117206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b172f1f-5040-4174-8043-ba9ba5bed64f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021172065.1_ASM2117206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:04:29,017] [INFO] Task succeeded: Blastn [2024-01-24 14:04:29,020] [INFO] Selected 13 target genomes. [2024-01-24 14:04:29,021] [INFO] Target genome list was writen to GCF_021172065.1_ASM2117206v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:04:29,035] [INFO] Task started: fastANI [2024-01-24 14:04:29,036] [INFO] Running command: fastANI --query /var/lib/cwl/stga2afd9cc-364d-4de8-a211-8b891571b568/GCF_021172065.1_ASM2117206v1_genomic.fna.gz --refList GCF_021172065.1_ASM2117206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021172065.1_ASM2117206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:04:43,660] [INFO] Task succeeded: fastANI [2024-01-24 14:04:43,676] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:04:43,676] [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_000330845.1 s__Pseudocitrobacter sp000330845 97.658 1440 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudocitrobacter 95.0 N/A N/A N/A N/A 1 conclusive GCF_008369545.1 s__Pseudocitrobacter sp008369545 93.7541 1405 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudocitrobacter 95.0 N/A N/A N/A N/A 1 - GCF_003315335.1 s__Pseudocitrobacter faecalis 92.7444 1389 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudocitrobacter 95.0 98.70 98.67 0.92 0.92 3 - GCF_014218705.1 s__Kluyvera sichuanensis 83.2009 1030 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 N/A N/A N/A N/A 1 - GCA_016939855.1 s__Kluyvera ascorbata_C 83.1136 582 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 N/A N/A N/A N/A 1 - GCF_014168815.1 s__Kluyvera ascorbata_B 83.0543 1057 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 99.36 99.08 0.90 0.88 9 - GCF_001654985.1 s__Kluyvera georgiana 83.029 1001 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 98.06 98.06 0.84 0.84 2 - GCA_002211745.1 s__Kluyvera georgiana_A 82.9857 1071 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 98.12 98.12 0.89 0.89 2 - GCF_000735365.1 s__Kluyvera ascorbata 82.9053 991 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera 95.0 98.94 97.70 0.94 0.89 5 - GCF_011754535.1 s__Enterobacter cloacae_N 82.2768 925 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.03 98.99 0.93 0.91 4 - GCF_005843885.1 s__Escherichia sp005843885 82.1327 864 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia 95.0 96.83 95.39 0.87 0.80 37 - GCF_000025565.1 s__Enterobacter cloacae 82.0002 944 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.05 95.14 0.91 0.80 129 - GCF_006539725.1 s__Klebsiella terrigena 81.6577 928 1671 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella 95.0 97.25 96.63 0.88 0.85 68 - -------------------------------------------------------------------------------- [2024-01-24 14:04:43,678] [INFO] GTDB search result was written to GCF_021172065.1_ASM2117206v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:04:43,679] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:04:43,682] [INFO] DFAST_QC result json was written to GCF_021172065.1_ASM2117206v1_genomic.fna/dqc_result.json [2024-01-24 14:04:43,682] [INFO] DFAST_QC completed! [2024-01-24 14:04:43,682] [INFO] Total running time: 0h1m35s