[2024-01-25 20:07:35,885] [INFO] DFAST_QC pipeline started. [2024-01-25 20:07:35,886] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 20:07:35,886] [INFO] DQC Reference Directory: /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference [2024-01-25 20:07:37,027] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 20:07:37,028] [INFO] Task started: Prodigal [2024-01-25 20:07:37,028] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0a8ea01-46a2-460b-bdc0-891b69b6818c/GCF_902806485.1_AiOr_genomic.fna.gz | prodigal -d GCF_902806485.1_AiOr_genomic.fna/cds.fna -a GCF_902806485.1_AiOr_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 20:07:48,606] [INFO] Task succeeded: Prodigal [2024-01-25 20:07:48,606] [INFO] Task started: HMMsearch [2024-01-25 20:07:48,606] [INFO] Running command: hmmsearch --tblout GCF_902806485.1_AiOr_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/reference_markers.hmm GCF_902806485.1_AiOr_genomic.fna/protein.faa > /dev/null [2024-01-25 20:07:48,859] [INFO] Task succeeded: HMMsearch [2024-01-25 20:07:48,860] [INFO] Found 6/6 markers. [2024-01-25 20:07:48,906] [INFO] Query marker FASTA was written to GCF_902806485.1_AiOr_genomic.fna/markers.fasta [2024-01-25 20:07:48,908] [INFO] Task started: Blastn [2024-01-25 20:07:48,908] [INFO] Running command: blastn -query GCF_902806485.1_AiOr_genomic.fna/markers.fasta -db /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/reference_markers.fasta -out GCF_902806485.1_AiOr_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:07:50,125] [INFO] Task succeeded: Blastn [2024-01-25 20:07:50,127] [INFO] Selected 6 target genomes. [2024-01-25 20:07:50,127] [INFO] Target genome list was writen to GCF_902806485.1_AiOr_genomic.fna/target_genomes.txt [2024-01-25 20:07:50,133] [INFO] Task started: fastANI [2024-01-25 20:07:50,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a8ea01-46a2-460b-bdc0-891b69b6818c/GCF_902806485.1_AiOr_genomic.fna.gz --refList GCF_902806485.1_AiOr_genomic.fna/target_genomes.txt --output GCF_902806485.1_AiOr_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 20:07:59,585] [INFO] Task succeeded: fastANI [2024-01-25 20:07:59,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 20:07:59,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 20:07:59,592] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold) [2024-01-25 20:07:59,592] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 20:07:59,592] [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 100.0 1533 1548 95 conclusive Frankia torreyi strain=CpI1 GCA_000948395.1 1856 1856 type True 90.713 1359 1548 95 below_threshold Frankia alni strain=ACN14a GCA_000058485.1 1859 1859 type True 89.9794 1310 1548 95 below_threshold Frankia canadensis GCA_900197875.1 1836972 1836972 type True 83.1477 1020 1548 95 below_threshold Frankia casuarinae strain=CcI3 GCA_000013345.1 106370 106370 type True 81.7717 859 1548 95 below_threshold Frankia elaeagni strain=BMG5.12 GCA_000374165.1 222534 222534 type True 79.2925 722 1548 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 20:07:59,593] [INFO] DFAST Taxonomy check result was written to GCF_902806485.1_AiOr_genomic.fna/tc_result.tsv [2024-01-25 20:07:59,594] [INFO] ===== Taxonomy check completed ===== [2024-01-25 20:07:59,594] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 20:07:59,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/checkm_data [2024-01-25 20:07:59,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 20:07:59,649] [INFO] Task started: CheckM [2024-01-25 20:07:59,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902806485.1_AiOr_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902806485.1_AiOr_genomic.fna/checkm_input GCF_902806485.1_AiOr_genomic.fna/checkm_result [2024-01-25 20:08:34,672] [INFO] Task succeeded: CheckM [2024-01-25 20:08:34,673] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 20:08:34,704] [INFO] ===== Completeness check finished ===== [2024-01-25 20:08:34,705] [INFO] ===== Start GTDB Search ===== [2024-01-25 20:08:34,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902806485.1_AiOr_genomic.fna/markers.fasta) [2024-01-25 20:08:34,706] [INFO] Task started: Blastn [2024-01-25 20:08:34,706] [INFO] Running command: blastn -query GCF_902806485.1_AiOr_genomic.fna/markers.fasta -db /var/lib/cwl/stgd22f1183-ea4f-4892-a59a-047d3fd1dc5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_902806485.1_AiOr_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:08:36,713] [INFO] Task succeeded: Blastn [2024-01-25 20:08:36,715] [INFO] Selected 7 target genomes. [2024-01-25 20:08:36,716] [INFO] Target genome list was writen to GCF_902806485.1_AiOr_genomic.fna/target_genomes_gtdb.txt [2024-01-25 20:08:36,725] [INFO] Task started: fastANI [2024-01-25 20:08:36,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a8ea01-46a2-460b-bdc0-891b69b6818c/GCF_902806485.1_AiOr_genomic.fna.gz --refList GCF_902806485.1_AiOr_genomic.fna/target_genomes_gtdb.txt --output GCF_902806485.1_AiOr_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 20:08:47,441] [INFO] Task succeeded: fastANI [2024-01-25 20:08:47,446] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 20:08:47,447] [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 100.0 1533 1548 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 conclusive GCF_000262465.1 s__Frankia sp000262465 90.7927 1327 1548 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 90.6774 1362 1548 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 89.9686 1310 1548 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 83.1035 1025 1548 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 100.00 100.00 0.99 0.99 2 - GCF_902806475.1 s__Frankia nodulisporulans 81.9115 804 1548 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.88 99.87 0.86 0.85 3 - GCF_000013345.1 s__Frankia casuarinae 81.7779 859 1548 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.59 99.21 0.94 0.87 12 - -------------------------------------------------------------------------------- [2024-01-25 20:08:47,448] [INFO] GTDB search result was written to GCF_902806485.1_AiOr_genomic.fna/result_gtdb.tsv [2024-01-25 20:08:47,448] [INFO] ===== GTDB Search completed ===== [2024-01-25 20:08:47,450] [INFO] DFAST_QC result json was written to GCF_902806485.1_AiOr_genomic.fna/dqc_result.json [2024-01-25 20:08:47,451] [INFO] DFAST_QC completed! [2024-01-25 20:08:47,451] [INFO] Total running time: 0h1m12s