[2024-01-24 12:21:44,782] [INFO] DFAST_QC pipeline started. [2024-01-24 12:21:44,784] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:21:44,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference [2024-01-24 12:21:46,132] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:21:46,132] [INFO] Task started: Prodigal [2024-01-24 12:21:46,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg753e98b5-76b8-4898-b3fb-42c9d21c2aba/GCF_025403405.1_ASM2540340v1_genomic.fna.gz | prodigal -d GCF_025403405.1_ASM2540340v1_genomic.fna/cds.fna -a GCF_025403405.1_ASM2540340v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:22:02,730] [INFO] Task succeeded: Prodigal [2024-01-24 12:22:02,730] [INFO] Task started: HMMsearch [2024-01-24 12:22:02,731] [INFO] Running command: hmmsearch --tblout GCF_025403405.1_ASM2540340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/reference_markers.hmm GCF_025403405.1_ASM2540340v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:22:03,124] [INFO] Task succeeded: HMMsearch [2024-01-24 12:22:03,125] [INFO] Found 6/6 markers. [2024-01-24 12:22:03,184] [INFO] Query marker FASTA was written to GCF_025403405.1_ASM2540340v1_genomic.fna/markers.fasta [2024-01-24 12:22:03,185] [INFO] Task started: Blastn [2024-01-24 12:22:03,185] [INFO] Running command: blastn -query GCF_025403405.1_ASM2540340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/reference_markers.fasta -out GCF_025403405.1_ASM2540340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:22:04,486] [INFO] Task succeeded: Blastn [2024-01-24 12:22:04,490] [INFO] Selected 11 target genomes. [2024-01-24 12:22:04,491] [INFO] Target genome list was writen to GCF_025403405.1_ASM2540340v1_genomic.fna/target_genomes.txt [2024-01-24 12:22:04,496] [INFO] Task started: fastANI [2024-01-24 12:22:04,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg753e98b5-76b8-4898-b3fb-42c9d21c2aba/GCF_025403405.1_ASM2540340v1_genomic.fna.gz --refList GCF_025403405.1_ASM2540340v1_genomic.fna/target_genomes.txt --output GCF_025403405.1_ASM2540340v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:22:24,169] [INFO] Task succeeded: fastANI [2024-01-24 12:22:24,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:22:24,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:22:24,180] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold) [2024-01-24 12:22:24,181] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 12:22:24,181] [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 93.9888 1197 1959 95 below_threshold Frankia torreyi strain=CpI1 GCA_000948395.1 1856 1856 type True 90.5742 1562 1959 95 below_threshold Frankia alni strain=ACN14a GCA_000058485.1 1859 1859 type True 89.848 1533 1959 95 below_threshold Frankia canadensis GCA_900197875.1 1836972 1836972 type True 82.7063 1108 1959 95 below_threshold Frankia casuarinae strain=CcI3 GCA_000013345.1 106370 106370 type True 81.6702 920 1959 95 below_threshold Frankia soli strain=NRRL B-16219 GCA_001854695.1 2599596 2599596 type True 79.3274 881 1959 95 below_threshold Frankia discariae strain=BCU110501 GCA_000373365.1 365528 365528 type True 79.3079 893 1959 95 below_threshold Frankia elaeagni strain=BMG5.12 GCA_000374165.1 222534 222534 type True 79.171 832 1959 95 below_threshold Frankia irregularis strain=DSM 45899 GCA_001536285.1 795642 795642 type True 78.8267 874 1959 95 below_threshold Frankia inefficax strain=EuI1c GCA_000166135.1 298654 298654 type True 78.3276 845 1959 95 below_threshold Amycolatopsis azurea strain=DSM 43854 GCA_000340415.1 36819 36819 type True 75.639 378 1959 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:22:24,184] [INFO] DFAST Taxonomy check result was written to GCF_025403405.1_ASM2540340v1_genomic.fna/tc_result.tsv [2024-01-24 12:22:24,184] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:22:24,185] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:22:24,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/checkm_data [2024-01-24 12:22:24,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:22:24,263] [INFO] Task started: CheckM [2024-01-24 12:22:24,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025403405.1_ASM2540340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025403405.1_ASM2540340v1_genomic.fna/checkm_input GCF_025403405.1_ASM2540340v1_genomic.fna/checkm_result [2024-01-24 12:23:15,439] [INFO] Task succeeded: CheckM [2024-01-24 12:23:15,440] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.38% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:23:15,471] [INFO] ===== Completeness check finished ===== [2024-01-24 12:23:15,472] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:23:15,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025403405.1_ASM2540340v1_genomic.fna/markers.fasta) [2024-01-24 12:23:15,472] [INFO] Task started: Blastn [2024-01-24 12:23:15,473] [INFO] Running command: blastn -query GCF_025403405.1_ASM2540340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07e0e650-f14c-4379-bda4-7e052fb1fbf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_025403405.1_ASM2540340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:23:17,513] [INFO] Task succeeded: Blastn [2024-01-24 12:23:17,516] [INFO] Selected 12 target genomes. [2024-01-24 12:23:17,516] [INFO] Target genome list was writen to GCF_025403405.1_ASM2540340v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:23:17,527] [INFO] Task started: fastANI [2024-01-24 12:23:17,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg753e98b5-76b8-4898-b3fb-42c9d21c2aba/GCF_025403405.1_ASM2540340v1_genomic.fna.gz --refList GCF_025403405.1_ASM2540340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025403405.1_ASM2540340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:23:37,341] [INFO] Task succeeded: fastANI [2024-01-24 12:23:37,356] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 12:23:37,356] [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 94.0834 1192 1959 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 90.635 1487 1959 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 90.6063 1558 1959 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 89.8662 1531 1959 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 82.7403 1104 1959 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 81.6469 923 1959 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.59 99.21 0.94 0.87 12 - GCF_001854655.1 s__Frankia sp001854655 79.3279 862 1959 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - GCF_000373365.1 s__Frankia discariae 79.295 895 1959 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 79.2119 823 1959 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 78.8742 864 1959 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 97.56 96.33 0.90 0.84 4 - GCF_016786355.1 s__Frankia sp016786355 78.4139 800 1959 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 99.92 99.92 0.97 0.97 3 - GCF_000166135.1 s__Frankia inefficax 78.3517 841 1959 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:23:37,359] [INFO] GTDB search result was written to GCF_025403405.1_ASM2540340v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:23:37,359] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:23:37,365] [INFO] DFAST_QC result json was written to GCF_025403405.1_ASM2540340v1_genomic.fna/dqc_result.json [2024-01-24 12:23:37,365] [INFO] DFAST_QC completed! [2024-01-24 12:23:37,365] [INFO] Total running time: 0h1m53s