[2024-01-24 12:05:26,614] [INFO] DFAST_QC pipeline started. [2024-01-24 12:05:26,622] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:05:26,622] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference [2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:05:30,678] [INFO] Task started: Prodigal [2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg7644359d-0cfb-4529-902d-a70a38dffeaa/GCF_913566895.1_201901311_genomic.fna.gz | prodigal -d GCF_913566895.1_201901311_genomic.fna/cds.fna -a GCF_913566895.1_201901311_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:05:38,092] [INFO] Task succeeded: Prodigal [2024-01-24 12:05:38,092] [INFO] Task started: HMMsearch [2024-01-24 12:05:38,092] [INFO] Running command: hmmsearch --tblout GCF_913566895.1_201901311_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/reference_markers.hmm GCF_913566895.1_201901311_genomic.fna/protein.faa > /dev/null [2024-01-24 12:05:38,348] [INFO] Task succeeded: HMMsearch [2024-01-24 12:05:38,349] [INFO] Found 6/6 markers. [2024-01-24 12:05:38,378] [INFO] Query marker FASTA was written to GCF_913566895.1_201901311_genomic.fna/markers.fasta [2024-01-24 12:05:38,379] [INFO] Task started: Blastn [2024-01-24 12:05:38,379] [INFO] Running command: blastn -query GCF_913566895.1_201901311_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/reference_markers.fasta -out GCF_913566895.1_201901311_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:05:38,993] [INFO] Task succeeded: Blastn [2024-01-24 12:05:38,996] [INFO] Selected 20 target genomes. [2024-01-24 12:05:38,997] [INFO] Target genome list was writen to GCF_913566895.1_201901311_genomic.fna/target_genomes.txt [2024-01-24 12:05:39,036] [INFO] Task started: fastANI [2024-01-24 12:05:39,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg7644359d-0cfb-4529-902d-a70a38dffeaa/GCF_913566895.1_201901311_genomic.fna.gz --refList GCF_913566895.1_201901311_genomic.fna/target_genomes.txt --output GCF_913566895.1_201901311_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:05:49,011] [INFO] Task succeeded: fastANI [2024-01-24 12:05:49,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:05:49,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:05:49,027] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold) [2024-01-24 12:05:49,027] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:05:49,027] [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 Listeria ilorinensis GCA_913566895.1 2867439 2867439 type True 100.0 990 991 95 conclusive Listeria costaricensis GCA_900183385.1 2026604 2026604 type True 85.1962 771 991 95 below_threshold Listeria fleischmannii subsp. fleischmannii strain=LU2006-1 GCA_000344175.1 1671902 1069827 type True 78.1228 173 991 95 below_threshold Listeria aquatica strain=FSL S10-1188 GCA_000525795.1 1494960 1494960 type True 78.0951 145 991 95 below_threshold Listeria floridensis strain=FSL S10-1187 GCA_000525875.1 1494962 1494962 type True 78.0776 159 991 95 below_threshold Listeria fleischmannii subsp. coloradonensis strain=NCTC13938 GCA_900452975.1 1081736 1069827 type True 78.0697 175 991 95 below_threshold Listeria goaensis strain=ILCC801 GCA_900186125.1 1649188 1649188 type True 77.938 169 991 95 below_threshold Listeria fleischmannii subsp. coloradonensis strain=TTU M1-001 GCA_000252625.2 1081736 1069827 type True 77.8417 154 991 95 below_threshold Listeria seeligeri strain=SLCC3954 GCA_000027145.1 1640 1640 type True 77.6377 175 991 95 below_threshold Listeria welshimeri strain=SLCC5334 GCA_000060285.1 1643 1643 type True 77.6303 173 991 95 below_threshold Listeria welshimeri strain=NCTC11857 GCA_900187315.1 1643 1643 type True 77.5852 172 991 95 below_threshold Listeria monocytogenes strain=2014L-6393 GCA_013626145.1 1639 1639 claderef True 77.4497 170 991 95 below_threshold Listeria monocytogenes strain=2014L-6256 GCA_013625895.1 1639 1639 claderef True 77.4324 191 991 95 below_threshold Listeria booriae strain=NCTC13936 GCA_900453065.1 1552123 1552123 type True 77.3519 110 991 95 below_threshold Listeria rocourtiae strain=FSL F6-920 GCA_000525975.1 647910 647910 type True 77.3303 113 991 95 below_threshold Listeria booriae strain=FSL A5-0281 GCA_000766865.1 1552123 1552123 type True 77.2692 109 991 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:05:49,029] [INFO] DFAST Taxonomy check result was written to GCF_913566895.1_201901311_genomic.fna/tc_result.tsv [2024-01-24 12:05:49,030] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:05:49,030] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:05:49,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/checkm_data [2024-01-24 12:05:49,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:05:49,066] [INFO] Task started: CheckM [2024-01-24 12:05:49,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_913566895.1_201901311_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_913566895.1_201901311_genomic.fna/checkm_input GCF_913566895.1_201901311_genomic.fna/checkm_result [2024-01-24 12:06:17,399] [INFO] Task succeeded: CheckM [2024-01-24 12:06:17,401] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:06:17,422] [INFO] ===== Completeness check finished ===== [2024-01-24 12:06:17,422] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:06:17,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_913566895.1_201901311_genomic.fna/markers.fasta) [2024-01-24 12:06:17,423] [INFO] Task started: Blastn [2024-01-24 12:06:17,423] [INFO] Running command: blastn -query GCF_913566895.1_201901311_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d14338-e9ff-4180-9366-1d5dd3856099/dqc_reference/reference_markers_gtdb.fasta -out GCF_913566895.1_201901311_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:06:18,197] [INFO] Task succeeded: Blastn [2024-01-24 12:06:18,200] [INFO] Selected 21 target genomes. [2024-01-24 12:06:18,200] [INFO] Target genome list was writen to GCF_913566895.1_201901311_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:06:18,209] [INFO] Task started: fastANI [2024-01-24 12:06:18,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg7644359d-0cfb-4529-902d-a70a38dffeaa/GCF_913566895.1_201901311_genomic.fna.gz --refList GCF_913566895.1_201901311_genomic.fna/target_genomes_gtdb.txt --output GCF_913566895.1_201901311_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:06:28,144] [INFO] Task succeeded: fastANI [2024-01-24 12:06:28,159] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 12:06:28,159] [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_900183385.1 s__Listeria costaricensis 85.1962 771 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 N/A N/A N/A N/A 1 - GCF_000344175.1 s__Listeria fleischmannii 78.1228 173 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 96.87 95.72 0.93 0.89 9 - GCF_000525875.1 s__Listeria floridensis 78.0776 159 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 N/A N/A N/A N/A 1 - GCF_000525795.1 s__Listeria aquatica 78.0695 146 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 97.71 97.71 0.93 0.93 2 - GCF_011800755.1 s__Listeria valentina 77.9742 147 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 N/A N/A N/A N/A 1 - GCF_900186125.1 s__Listeria goaensis 77.938 169 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 99.59 99.37 0.97 0.94 8 - GCF_000763495.1 s__Listeria londoniensis 77.8166 179 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 99.36 98.73 0.96 0.94 17 - GCF_900187025.1 s__Listeria ivanovii 77.7223 177 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 99.75 99.44 0.99 0.97 26 - GCF_014229095.1 s__Listeria cayugensis 77.667 177 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 97.39 97.39 0.93 0.93 2 - GCF_000027145.1 s__Listeria seeligeri 77.6564 174 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 97.08 96.23 0.92 0.88 167 - GCF_000060285.1 s__Listeria welshimeri 77.6116 174 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 98.96 98.73 0.93 0.90 49 - GCF_014229245.1 s__Listeria farberi 77.6039 171 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 99.35 99.31 0.93 0.92 5 - GCF_014224155.1 s__Listeria cossartiae 77.5796 176 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 98.01 97.44 0.96 0.94 9 - GCA_000183865.1 s__Listeria marthii 77.5722 178 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 98.26 98.03 0.95 0.91 34 - GCF_013282665.1 s__Listeria monocytogenes_C 77.5352 190 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 95.79 95.20 0.93 0.91 176 - GCF_014229645.1 s__Listeria sp014229645 77.4989 184 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 N/A N/A N/A N/A 1 - GCF_900187225.1 s__Listeria monocytogenes 77.4583 187 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria 95.0 99.04 95.98 0.97 0.89 1977 - GCF_000525995.1 s__Listeria_A riparia 77.423 105 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A 95.0 N/A N/A N/A N/A 1 - GCF_000766865.1 s__Listeria_A booriae 77.2692 109 991 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A 95.0 97.10 95.37 0.89 0.81 92 - -------------------------------------------------------------------------------- [2024-01-24 12:06:28,167] [INFO] GTDB search result was written to GCF_913566895.1_201901311_genomic.fna/result_gtdb.tsv [2024-01-24 12:06:28,168] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:06:28,172] [INFO] DFAST_QC result json was written to GCF_913566895.1_201901311_genomic.fna/dqc_result.json [2024-01-24 12:06:28,172] [INFO] DFAST_QC completed! [2024-01-24 12:06:28,172] [INFO] Total running time: 0h1m2s