[2023-06-27 20:56:54,717] [INFO] DFAST_QC pipeline started. [2023-06-27 20:56:54,720] [INFO] DFAST_QC version: 0.5.7 [2023-06-27 20:56:54,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference [2023-06-27 20:56:56,077] [INFO] ===== Start taxonomy check using ANI ===== [2023-06-27 20:56:56,078] [INFO] Task started: Prodigal [2023-06-27 20:56:56,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cac9c62-1f58-4ba3-9957-3bea940d5f84/GCA_002430365.1_ASM243036v1_genomic.fna.gz | prodigal -d GCA_002430365.1_ASM243036v1_genomic.fna/cds.fna -a GCA_002430365.1_ASM243036v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2023-06-27 20:57:08,454] [INFO] Task succeeded: Prodigal [2023-06-27 20:57:08,454] [INFO] Task started: HMMsearch [2023-06-27 20:57:08,454] [INFO] Running command: hmmsearch --tblout GCA_002430365.1_ASM243036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/reference_markers.hmm GCA_002430365.1_ASM243036v1_genomic.fna/protein.faa > /dev/null [2023-06-27 20:57:08,780] [INFO] Task succeeded: HMMsearch [2023-06-27 20:57:08,781] [INFO] Found 6/6 markers. [2023-06-27 20:57:08,821] [INFO] Query marker FASTA was written to GCA_002430365.1_ASM243036v1_genomic.fna/markers.fasta [2023-06-27 20:57:08,822] [INFO] Task started: Blastn [2023-06-27 20:57:08,822] [INFO] Running command: blastn -query GCA_002430365.1_ASM243036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/reference_markers.fasta -out GCA_002430365.1_ASM243036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-27 20:57:09,710] [INFO] Task succeeded: Blastn [2023-06-27 20:57:09,723] [INFO] Selected 18 target genomes. [2023-06-27 20:57:09,723] [INFO] Target genome list was writen to GCA_002430365.1_ASM243036v1_genomic.fna/target_genomes.txt [2023-06-27 20:57:09,743] [INFO] Task started: fastANI [2023-06-27 20:57:09,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cac9c62-1f58-4ba3-9957-3bea940d5f84/GCA_002430365.1_ASM243036v1_genomic.fna.gz --refList GCA_002430365.1_ASM243036v1_genomic.fna/target_genomes.txt --output GCA_002430365.1_ASM243036v1_genomic.fna/fastani_result.tsv --threads 1 [2023-06-27 20:57:27,127] [INFO] Task succeeded: fastANI [2023-06-27 20:57:27,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2023-06-27 20:57:27,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2023-06-27 20:57:27,145] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold) [2023-06-27 20:57:27,145] [INFO] The taxonomy check result is classified as 'conclusive'. [2023-06-27 20:57:27,145] [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_018987305.1 2815358 2815358 type True 98.5184 1355 1478 95 conclusive Leclercia pneumoniae strain=49125 GCA_017348915.1 2815358 2815358 type True 98.5143 1357 1478 95 conclusive Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 84.7766 1055 1478 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 84.5988 1058 1478 95 below_threshold Enterobacter wuhouensis strain=WCHEW120002 GCA_004331265.1 2529381 2529381 type True 84.2541 1082 1478 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 84.2393 999 1478 95 below_threshold Leclercia adecarboxylata strain=FDAARGOS_1505 GCA_020097395.1 83655 83655 suspected-type True 84.2257 1139 1478 95 below_threshold Leclercia adecarboxylata strain=ATCC 23216 GCA_000735515.1 83655 83655 suspected-type True 84.2122 1122 1478 95 below_threshold Leclercia adecarboxylata strain=NBRC 102595 GCA_001515505.1 83655 83655 suspected-type True 84.2 1124 1478 95 below_threshold Enterobacter oligotrophicus strain=CCA6 GCA_009176645.1 2478464 2478464 type True 84.0804 1042 1478 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 84.0389 1076 1478 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 83.9952 1059 1478 95 below_threshold Enterobacter hormaechei subsp. hoffmannii strain=DSM 14563 GCA_001729745.1 1812934 158836 type True 83.9329 1031 1478 95 below_threshold Enterobacter hormaechei subsp. hormaechei strain=ATCC 49162 GCA_001875655.1 301105 158836 type True 83.9136 1049 1478 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 83.857 1047 1478 95 below_threshold -------------------------------------------------------------------------------- [2023-06-27 20:57:27,147] [INFO] DFAST Taxonomy check result was written to GCA_002430365.1_ASM243036v1_genomic.fna/tc_result.tsv [2023-06-27 20:57:27,148] [INFO] ===== Taxonomy check completed ===== [2023-06-27 20:57:27,148] [INFO] ===== Start completeness check using CheckM ===== [2023-06-27 20:57:27,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/checkm_data [2023-06-27 20:57:27,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2023-06-27 20:57:27,196] [INFO] Task started: CheckM [2023-06-27 20:57:27,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002430365.1_ASM243036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002430365.1_ASM243036v1_genomic.fna/checkm_input GCA_002430365.1_ASM243036v1_genomic.fna/checkm_result [2023-06-27 20:58:06,508] [INFO] Task succeeded: CheckM [2023-06-27 20:58:06,510] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 79.17% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2023-06-27 20:58:06,531] [INFO] ===== Completeness check finished ===== [2023-06-27 20:58:06,531] [INFO] ===== Start GTDB Search ===== [2023-06-27 20:58:06,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002430365.1_ASM243036v1_genomic.fna/markers.fasta) [2023-06-27 20:58:06,532] [INFO] Task started: Blastn [2023-06-27 20:58:06,532] [INFO] Running command: blastn -query GCA_002430365.1_ASM243036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6acf9f-7772-4a22-9c8e-5f65d5918a43/dqc_reference/reference_markers_gtdb.fasta -out GCA_002430365.1_ASM243036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-27 20:58:07,675] [INFO] Task succeeded: Blastn [2023-06-27 20:58:07,679] [INFO] Selected 24 target genomes. [2023-06-27 20:58:07,679] [INFO] Target genome list was writen to GCA_002430365.1_ASM243036v1_genomic.fna/target_genomes_gtdb.txt [2023-06-27 20:58:07,717] [INFO] Task started: fastANI [2023-06-27 20:58:07,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cac9c62-1f58-4ba3-9957-3bea940d5f84/GCA_002430365.1_ASM243036v1_genomic.fna.gz --refList GCA_002430365.1_ASM243036v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002430365.1_ASM243036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2023-06-27 20:58:30,694] [INFO] Task succeeded: fastANI [2023-06-27 20:58:30,717] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2023-06-27 20:58:30,717] [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 98.5143 1357 1478 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 85.4889 812 1478 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 84.7558 1058 1478 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 84.4674 1124 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 97.80 96.55 0.92 0.89 4 - GCF_006874705.1 s__Leclercia adecarboxylata_C 84.4584 1132 1478 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 84.44 1124 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 99.97 99.97 0.98 0.98 2 - GCF_011290365.1 s__Leclercia sp003024485 84.4247 1114 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.06 98.06 0.90 0.90 2 - GCF_004331265.1 s__Enterobacter wuhouensis 84.2632 1081 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_003594935.1 s__Enterobacter huaxiensis 84.254 1070 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.98 98.98 0.94 0.94 2 - GCF_008364625.1 s__Enterobacter dykesii 84.2249 1025 1478 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 84.0976 1135 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia 95.0 98.53 98.09 0.95 0.87 86 - GCF_007035645.1 s__Enterobacter asburiae_B 84.0839 1045 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.31 97.34 0.92 0.85 70 - GCF_009176645.1 s__Enterobacter oligotrophicus 84.0699 1043 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 99.55 99.09 0.97 0.94 3 - GCF_009755685.1 s__Enterobacter sp000568095 84.062 1038 1478 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 84.0468 1043 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 98.32 0.92 0.92 3 - GCF_000211415.1 s__Enterobacter mori 84.0383 1051 1478 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 83.9948 1034 1478 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 83.9353 1031 1478 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 83.8341 993 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_018257515.1 s__Tatumella sp018257515 77.9733 196 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella 95.0 N/A N/A N/A N/A 1 - GCF_015548865.1 s__Symbiopectobacterium marcescens_A 77.8907 237 1478 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Symbiopectobacterium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2023-06-27 20:58:30,719] [INFO] GTDB search result was written to GCA_002430365.1_ASM243036v1_genomic.fna/result_gtdb.tsv [2023-06-27 20:58:30,720] [INFO] ===== GTDB Search completed ===== [2023-06-27 20:58:30,724] [INFO] DFAST_QC result json was written to GCA_002430365.1_ASM243036v1_genomic.fna/dqc_result.json [2023-06-27 20:58:30,724] [INFO] DFAST_QC completed! [2023-06-27 20:58:30,724] [INFO] Total running time: 0h1m36s