[2024-01-24 12:15:04,197] [INFO] DFAST_QC pipeline started. [2024-01-24 12:15:04,202] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:15:04,202] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference [2024-01-24 12:15:05,514] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:15:05,515] [INFO] Task started: Prodigal [2024-01-24 12:15:05,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgabf46e55-5c71-4637-ad2e-90584491a98e/GCF_003594935.2_ASM359493v2_genomic.fna.gz | prodigal -d GCF_003594935.2_ASM359493v2_genomic.fna/cds.fna -a GCF_003594935.2_ASM359493v2_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:15:21,225] [INFO] Task succeeded: Prodigal [2024-01-24 12:15:21,226] [INFO] Task started: HMMsearch [2024-01-24 12:15:21,226] [INFO] Running command: hmmsearch --tblout GCF_003594935.2_ASM359493v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/reference_markers.hmm GCF_003594935.2_ASM359493v2_genomic.fna/protein.faa > /dev/null [2024-01-24 12:15:21,576] [INFO] Task succeeded: HMMsearch [2024-01-24 12:15:21,579] [INFO] Found 6/6 markers. [2024-01-24 12:15:21,631] [INFO] Query marker FASTA was written to GCF_003594935.2_ASM359493v2_genomic.fna/markers.fasta [2024-01-24 12:15:21,631] [INFO] Task started: Blastn [2024-01-24 12:15:21,631] [INFO] Running command: blastn -query GCF_003594935.2_ASM359493v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/reference_markers.fasta -out GCF_003594935.2_ASM359493v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:15:22,552] [INFO] Task succeeded: Blastn [2024-01-24 12:15:22,557] [INFO] Selected 17 target genomes. [2024-01-24 12:15:22,557] [INFO] Target genome list was writen to GCF_003594935.2_ASM359493v2_genomic.fna/target_genomes.txt [2024-01-24 12:15:22,569] [INFO] Task started: fastANI [2024-01-24 12:15:22,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf46e55-5c71-4637-ad2e-90584491a98e/GCF_003594935.2_ASM359493v2_genomic.fna.gz --refList GCF_003594935.2_ASM359493v2_genomic.fna/target_genomes.txt --output GCF_003594935.2_ASM359493v2_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:15:41,343] [INFO] Task succeeded: fastANI [2024-01-24 12:15:41,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:15:41,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:15:41,364] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold) [2024-01-24 12:15:41,364] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 12:15:41,365] [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 90.6547 1380 1679 95 below_threshold Enterobacter quasimori strain=090044 GCA_003964905.1 2838947 2838947 type True 89.7924 1329 1679 95 below_threshold Enterobacter mori strain=LMG 25706 GCA_000211415.1 539813 539813 type True 89.7346 1309 1679 95 below_threshold Enterobacter asburiae strain=FDAARGOS_892 GCA_016027695.1 61645 61645 type True 89.1932 1244 1679 95 below_threshold Enterobacter asburiae strain=ATCC 35953 GCA_001521715.1 61645 61645 type True 89.1727 1249 1679 95 below_threshold Enterobacter bugandensis GCA_900324475.1 881260 881260 type True 88.8433 1308 1679 95 below_threshold Enterobacter bugandensis strain=FDAARGOS 1427 GCA_019046905.1 881260 881260 type True 88.7817 1319 1679 95 below_threshold Enterobacter roggenkampii strain=DSM 16690 GCA_024390995.1 1812935 1812935 type True 88.7271 1202 1679 95 below_threshold Enterobacter chengduensis strain=WCHECl-C4 = WCHECh050004 GCA_001984825.2 2494701 2494701 type True 88.7142 1299 1679 95 below_threshold Enterobacter vonholyi strain=E13 GCA_008364555.1 2797505 2797505 type True 88.5482 1251 1679 95 below_threshold Enterobacter oligotrophicus strain=CCA6 GCA_009176645.1 2478464 2478464 type True 88.5349 1281 1679 95 below_threshold Enterobacter hormaechei strain=FDAARGOS 1433 GCA_019048245.1 158836 158836 suspected-type True 88.1622 1300 1679 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_002939185.1 2071710 2071710 type True 87.9248 1197 1679 95 below_threshold Enterobacter sichuanensis strain=WCHECL1597 GCA_025002605.1 2071710 2071710 type True 87.8589 1261 1679 95 below_threshold Enterobacter cloacae strain=DSM 30054 GCA_021469225.1 550 550 type True 87.5545 1328 1679 95 below_threshold Enterobacter cancerogenus strain=FDAARGOS 1428 GCA_019047785.1 69218 69218 type True 87.5443 1286 1679 95 below_threshold Enterobacter cancerogenus GCA_900185905.1 69218 69218 type True 87.4042 1279 1679 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:15:41,366] [INFO] DFAST Taxonomy check result was written to GCF_003594935.2_ASM359493v2_genomic.fna/tc_result.tsv [2024-01-24 12:15:41,367] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:15:41,367] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:15:41,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/checkm_data [2024-01-24 12:15:41,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:15:41,417] [INFO] Task started: CheckM [2024-01-24 12:15:41,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003594935.2_ASM359493v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003594935.2_ASM359493v2_genomic.fna/checkm_input GCF_003594935.2_ASM359493v2_genomic.fna/checkm_result [2024-01-24 12:16:27,841] [INFO] Task succeeded: CheckM [2024-01-24 12:16:27,842] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 98.96% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:16:27,869] [INFO] ===== Completeness check finished ===== [2024-01-24 12:16:27,870] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:16:27,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003594935.2_ASM359493v2_genomic.fna/markers.fasta) [2024-01-24 12:16:27,870] [INFO] Task started: Blastn [2024-01-24 12:16:27,871] [INFO] Running command: blastn -query GCF_003594935.2_ASM359493v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f3f3a0d-e0ea-4ed5-9849-f6181a1912d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003594935.2_ASM359493v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:16:29,262] [INFO] Task succeeded: Blastn [2024-01-24 12:16:29,266] [INFO] Selected 15 target genomes. [2024-01-24 12:16:29,267] [INFO] Target genome list was writen to GCF_003594935.2_ASM359493v2_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:16:29,278] [INFO] Task started: fastANI [2024-01-24 12:16:29,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf46e55-5c71-4637-ad2e-90584491a98e/GCF_003594935.2_ASM359493v2_genomic.fna.gz --refList GCF_003594935.2_ASM359493v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003594935.2_ASM359493v2_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:16:46,171] [INFO] Task succeeded: fastANI [2024-01-24 12:16:46,188] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:16:46,189] [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_003594935.1 s__Enterobacter huaxiensis 99.965 1648 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.98 98.98 0.94 0.94 2 conclusive GCF_004331265.1 s__Enterobacter wuhouensis 90.6547 1380 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_000211415.1 s__Enterobacter mori 89.7346 1309 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.59 96.13 0.88 0.85 23 - GCF_000493015.1 s__Enterobacter sp000493015 89.2722 1309 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.7595 98.68 98.68 0.92 0.92 2 - GCF_003634515.1 s__Enterobacter asburiae_A 89.2096 1300 1679 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 89.1733 1249 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.8818 98.42 96.92 0.89 0.84 32 - GCF_008080435.1 s__Enterobacter asburiae_C 88.9571 1264 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.5575 N/A N/A N/A N/A 1 - GCF_900324475.1 s__Enterobacter bugandensis 88.8433 1308 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.49 95.52 0.94 0.88 115 - GCF_008364625.1 s__Enterobacter dykesii 88.8206 1268 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 96.5795 99.13 97.97 0.97 0.95 7 - GCF_003594915.1 s__Enterobacter chuandaensis 88.7982 1267 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 98.32 0.92 0.92 3 - GCF_001984825.2 s__Enterobacter chengduensis 88.7236 1298 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.11 95.58 0.88 0.79 24 - GCF_001022965.1 s__Enterobacter cloacae_L 88.5988 1340 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 97.51 97.16 0.91 0.90 5 - GCF_004402045.1 s__Enterobacter nimipressuralis_A 88.3532 1288 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - GCF_002939185.1 s__Enterobacter sichuanensis 87.9028 1199 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 98.38 97.99 0.90 0.85 19 - GCF_003057745.1 s__Enterobacter sp003057745 87.3375 1224 1679 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:16:46,190] [INFO] GTDB search result was written to GCF_003594935.2_ASM359493v2_genomic.fna/result_gtdb.tsv [2024-01-24 12:16:46,192] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:16:46,195] [INFO] DFAST_QC result json was written to GCF_003594935.2_ASM359493v2_genomic.fna/dqc_result.json [2024-01-24 12:16:46,196] [INFO] DFAST_QC completed! [2024-01-24 12:16:46,196] [INFO] Total running time: 0h1m42s