[2024-01-24 11:43:41,255] [INFO] DFAST_QC pipeline started. [2024-01-24 11:43:41,258] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:43:41,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference [2024-01-24 11:43:43,042] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:43:43,048] [INFO] Task started: Prodigal [2024-01-24 11:43:43,049] [INFO] Running command: gunzip -c /var/lib/cwl/stgda1deca8-2a7c-4e63-8e13-28de48ccf79d/GCF_025403375.1_ASM2540337v1_genomic.fna.gz | prodigal -d GCF_025403375.1_ASM2540337v1_genomic.fna/cds.fna -a GCF_025403375.1_ASM2540337v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:44:01,161] [INFO] Task succeeded: Prodigal [2024-01-24 11:44:01,162] [INFO] Task started: HMMsearch [2024-01-24 11:44:01,162] [INFO] Running command: hmmsearch --tblout GCF_025403375.1_ASM2540337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/reference_markers.hmm GCF_025403375.1_ASM2540337v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:44:01,572] [INFO] Task succeeded: HMMsearch [2024-01-24 11:44:01,574] [INFO] Found 6/6 markers. [2024-01-24 11:44:01,632] [INFO] Query marker FASTA was written to GCF_025403375.1_ASM2540337v1_genomic.fna/markers.fasta [2024-01-24 11:44:01,632] [INFO] Task started: Blastn [2024-01-24 11:44:01,632] [INFO] Running command: blastn -query GCF_025403375.1_ASM2540337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/reference_markers.fasta -out GCF_025403375.1_ASM2540337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:44:02,783] [INFO] Task succeeded: Blastn [2024-01-24 11:44:02,786] [INFO] Selected 9 target genomes. [2024-01-24 11:44:02,787] [INFO] Target genome list was writen to GCF_025403375.1_ASM2540337v1_genomic.fna/target_genomes.txt [2024-01-24 11:44:02,795] [INFO] Task started: fastANI [2024-01-24 11:44:02,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1deca8-2a7c-4e63-8e13-28de48ccf79d/GCF_025403375.1_ASM2540337v1_genomic.fna.gz --refList GCF_025403375.1_ASM2540337v1_genomic.fna/target_genomes.txt --output GCF_025403375.1_ASM2540337v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:44:18,416] [INFO] Task succeeded: fastANI [2024-01-24 11:44:18,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:44:18,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:44:18,427] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:44:18,427] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:44:18,427] [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 Candidatus Frankia alpina GCA_902806485.1 2699483 2699483 type True 93.9211 1246 2174 95 below_threshold Frankia torreyi strain=CpI1 GCA_000948395.1 1856 1856 type True 90.5302 1655 2174 95 below_threshold Frankia alni strain=ACN14a GCA_000058485.1 1859 1859 type True 89.9286 1665 2174 95 below_threshold Frankia canadensis GCA_900197875.1 1836972 1836972 type True 82.8481 1153 2174 95 below_threshold Frankia casuarinae strain=CcI3 GCA_000013345.1 106370 106370 type True 81.6488 952 2174 95 below_threshold Frankia soli strain=NRRL B-16219 GCA_001854695.1 2599596 2599596 type True 79.334 922 2174 95 below_threshold Frankia discariae strain=BCU110501 GCA_000373365.1 365528 365528 type True 79.2905 940 2174 95 below_threshold Frankia elaeagni strain=BMG5.12 GCA_000374165.1 222534 222534 type True 79.0983 868 2174 95 below_threshold Frankia irregularis strain=DSM 45899 GCA_001536285.1 795642 795642 type True 78.6744 931 2174 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:44:18,431] [INFO] DFAST Taxonomy check result was written to GCF_025403375.1_ASM2540337v1_genomic.fna/tc_result.tsv [2024-01-24 11:44:18,431] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:44:18,431] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:44:18,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/checkm_data [2024-01-24 11:44:18,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:44:18,504] [INFO] Task started: CheckM [2024-01-24 11:44:18,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025403375.1_ASM2540337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025403375.1_ASM2540337v1_genomic.fna/checkm_input GCF_025403375.1_ASM2540337v1_genomic.fna/checkm_result [2024-01-24 11:45:12,694] [INFO] Task succeeded: CheckM [2024-01-24 11:45:12,696] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:45:12,719] [INFO] ===== Completeness check finished ===== [2024-01-24 11:45:12,720] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:45:12,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025403375.1_ASM2540337v1_genomic.fna/markers.fasta) [2024-01-24 11:45:12,721] [INFO] Task started: Blastn [2024-01-24 11:45:12,721] [INFO] Running command: blastn -query GCF_025403375.1_ASM2540337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0450721-2237-4f0d-9bf0-39a2190ddec0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025403375.1_ASM2540337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:45:14,421] [INFO] Task succeeded: Blastn [2024-01-24 11:45:14,425] [INFO] Selected 9 target genomes. [2024-01-24 11:45:14,426] [INFO] Target genome list was writen to GCF_025403375.1_ASM2540337v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:45:14,434] [INFO] Task started: fastANI [2024-01-24 11:45:14,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1deca8-2a7c-4e63-8e13-28de48ccf79d/GCF_025403375.1_ASM2540337v1_genomic.fna.gz --refList GCF_025403375.1_ASM2540337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025403375.1_ASM2540337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:45:29,736] [INFO] Task succeeded: fastANI [2024-01-24 11:45:29,754] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 11:45:29,754] [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_902806485.1 s__Frankia sp902806485 93.8596 1250 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - GCF_000262465.1 s__Frankia sp000262465 90.7247 1655 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - GCF_000948395.1 s__Frankia torreyi 90.536 1655 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.67 99.51 0.95 0.92 3 - GCF_000058485.1 s__Frankia alni 89.9133 1667 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.50 99.50 0.95 0.95 2 - GCF_900197875.1 s__Frankia canadensis 82.8161 1158 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 100.00 100.00 0.99 0.99 2 - GCF_000013345.1 s__Frankia casuarinae 81.6304 954 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.59 99.21 0.94 0.87 12 - GCF_000373365.1 s__Frankia discariae 79.2558 947 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - GCF_000374165.1 s__Frankia elaeagni 79.1147 865 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - GCF_001536285.1 s__Frankia irregularis 78.6597 932 2174 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 97.56 96.33 0.90 0.84 4 - -------------------------------------------------------------------------------- [2024-01-24 11:45:29,756] [INFO] GTDB search result was written to GCF_025403375.1_ASM2540337v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:45:29,757] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:45:29,762] [INFO] DFAST_QC result json was written to GCF_025403375.1_ASM2540337v1_genomic.fna/dqc_result.json [2024-01-24 11:45:29,762] [INFO] DFAST_QC completed! [2024-01-24 11:45:29,762] [INFO] Total running time: 0h1m49s