[2024-01-24 14:14:47,072] [INFO] DFAST_QC pipeline started. [2024-01-24 14:14:47,075] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:14:47,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference [2024-01-24 14:14:49,422] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:14:49,423] [INFO] Task started: Prodigal [2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg5536bbbf-16f6-46f2-9144-298257f4d878/GCF_025998055.1_ASM2599805v1_genomic.fna.gz | prodigal -d GCF_025998055.1_ASM2599805v1_genomic.fna/cds.fna -a GCF_025998055.1_ASM2599805v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:14:54,678] [INFO] Task succeeded: Prodigal [2024-01-24 14:14:54,678] [INFO] Task started: HMMsearch [2024-01-24 14:14:54,678] [INFO] Running command: hmmsearch --tblout GCF_025998055.1_ASM2599805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/reference_markers.hmm GCF_025998055.1_ASM2599805v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:14:54,914] [INFO] Task succeeded: HMMsearch [2024-01-24 14:14:54,915] [INFO] Found 6/6 markers. [2024-01-24 14:14:54,935] [INFO] Query marker FASTA was written to GCF_025998055.1_ASM2599805v1_genomic.fna/markers.fasta [2024-01-24 14:14:54,935] [INFO] Task started: Blastn [2024-01-24 14:14:54,936] [INFO] Running command: blastn -query GCF_025998055.1_ASM2599805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/reference_markers.fasta -out GCF_025998055.1_ASM2599805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:14:57,105] [INFO] Task succeeded: Blastn [2024-01-24 14:14:57,111] [INFO] Selected 9 target genomes. [2024-01-24 14:14:57,111] [INFO] Target genome list was writen to GCF_025998055.1_ASM2599805v1_genomic.fna/target_genomes.txt [2024-01-24 14:14:57,224] [INFO] Task started: fastANI [2024-01-24 14:14:57,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg5536bbbf-16f6-46f2-9144-298257f4d878/GCF_025998055.1_ASM2599805v1_genomic.fna.gz --refList GCF_025998055.1_ASM2599805v1_genomic.fna/target_genomes.txt --output GCF_025998055.1_ASM2599805v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:15:00,470] [INFO] Task succeeded: fastANI [2024-01-24 14:15:00,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:15:00,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:15:00,483] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold) [2024-01-24 14:15:00,483] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:15:00,484] [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 Helicobacter heilmannii GCA_001283065.1 35817 35817 type True 99.862 539 552 95 conclusive Helicobacter heilmannii strain=LMG 26292 GCA_017979395.1 35817 35817 type True 99.8098 474 552 95 conclusive Helicobacter ailurogastricus GCA_001282945.1 1578720 1578720 type True 83.7895 414 552 95 below_threshold Helicobacter mehlei strain=L15 GCA_003660265.1 2316080 2316080 type True 78.6924 195 552 95 below_threshold Helicobacter bizzozeronii strain=CIP 105233 GCA_017979515.1 56877 56877 type True 78.1266 198 552 95 below_threshold Helicobacter vulpis strain=L2 GCA_003660395.1 2316076 2316076 type True 78.0853 161 552 95 below_threshold Helicobacter labacensis strain=L9 GCA_003660285.1 2316079 2316079 type True 77.6472 179 552 95 below_threshold Helicobacter suis strain=DSM 19735 GCA_017979375.1 104628 104628 type True 76.8091 106 552 95 below_threshold Helicobacter suis strain=HS1 GCA_000187625.2 104628 104628 type True 76.7059 113 552 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:15:00,485] [INFO] DFAST Taxonomy check result was written to GCF_025998055.1_ASM2599805v1_genomic.fna/tc_result.tsv [2024-01-24 14:15:00,486] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:15:00,486] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:15:00,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/checkm_data [2024-01-24 14:15:00,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:15:00,507] [INFO] Task started: CheckM [2024-01-24 14:15:00,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025998055.1_ASM2599805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025998055.1_ASM2599805v1_genomic.fna/checkm_input GCF_025998055.1_ASM2599805v1_genomic.fna/checkm_result [2024-01-24 14:15:25,729] [INFO] Task succeeded: CheckM [2024-01-24 14:15:25,730] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 95.83% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:15:25,749] [INFO] ===== Completeness check finished ===== [2024-01-24 14:15:25,749] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:15:25,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025998055.1_ASM2599805v1_genomic.fna/markers.fasta) [2024-01-24 14:15:25,750] [INFO] Task started: Blastn [2024-01-24 14:15:25,750] [INFO] Running command: blastn -query GCF_025998055.1_ASM2599805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf47133a3-3da9-4e95-b2a1-c8174624f820/dqc_reference/reference_markers_gtdb.fasta -out GCF_025998055.1_ASM2599805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:15:26,613] [INFO] Task succeeded: Blastn [2024-01-24 14:15:26,618] [INFO] Selected 12 target genomes. [2024-01-24 14:15:26,618] [INFO] Target genome list was writen to GCF_025998055.1_ASM2599805v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:15:26,637] [INFO] Task started: fastANI [2024-01-24 14:15:26,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg5536bbbf-16f6-46f2-9144-298257f4d878/GCF_025998055.1_ASM2599805v1_genomic.fna.gz --refList GCF_025998055.1_ASM2599805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025998055.1_ASM2599805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:15:30,487] [INFO] Task succeeded: fastANI [2024-01-24 14:15:30,496] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:15:30,497] [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_001283065.1 s__Helicobacter_E heilmannii 99.862 539 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.65 98.18 0.97 0.95 9 conclusive GCF_001282945.1 s__Helicobacter_E ailurogastricus 83.8165 413 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.41 98.32 0.95 0.92 6 - GCF_003660265.1 s__Helicobacter_E mehlei 78.7142 194 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 99.56 99.56 0.97 0.96 3 - GCA_000263275.1 s__Helicobacter_E bizzozeronii 78.3686 204 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 96.96 95.19 0.90 0.83 11 - GCF_000200595.1 s__Helicobacter_E felis 78.2428 157 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 97.57 97.30 0.96 0.93 23 - GCF_003660395.1 s__Helicobacter_E vulpis 78.1085 160 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 N/A N/A N/A N/A 1 - GCF_003660285.1 s__Helicobacter_E labacensis 77.6472 179 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 98.30 98.30 0.89 0.89 2 - GCF_902196135.1 s__Helicobacter_E suis_A 77.1838 101 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 97.68 97.34 0.95 0.91 4 - GCF_902196125.1 s__Helicobacter_E suis_B 77.0791 111 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 96.42 96.42 0.94 0.90 3 - GCF_000187625.1 s__Helicobacter_E suis 76.7059 113 552 d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E 95.0 99.74 99.56 0.96 0.89 27 - -------------------------------------------------------------------------------- [2024-01-24 14:15:30,498] [INFO] GTDB search result was written to GCF_025998055.1_ASM2599805v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:15:30,499] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:15:30,502] [INFO] DFAST_QC result json was written to GCF_025998055.1_ASM2599805v1_genomic.fna/dqc_result.json [2024-01-24 14:15:30,502] [INFO] DFAST_QC completed! [2024-01-24 14:15:30,502] [INFO] Total running time: 0h0m43s