[2024-01-25 18:52:20,626] [INFO] DFAST_QC pipeline started. [2024-01-25 18:52:20,628] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:52:20,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference [2024-01-25 18:52:21,819] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:52:21,820] [INFO] Task started: Prodigal [2024-01-25 18:52:21,820] [INFO] Running command: gunzip -c /var/lib/cwl/stgb17a0182-685a-415d-85fe-362da6566113/GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:52:45,180] [INFO] Task succeeded: Prodigal [2024-01-25 18:52:45,180] [INFO] Task started: HMMsearch [2024-01-25 18:52:45,180] [INFO] Running command: hmmsearch --tblout GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/reference_markers.hmm GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null [2024-01-25 18:52:45,496] [INFO] Task succeeded: HMMsearch [2024-01-25 18:52:45,497] [INFO] Found 6/6 markers. [2024-01-25 18:52:45,562] [INFO] Query marker FASTA was written to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta [2024-01-25 18:52:45,562] [INFO] Task started: Blastn [2024-01-25 18:52:45,562] [INFO] Running command: blastn -query GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/reference_markers.fasta -out GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:52:46,518] [INFO] Task succeeded: Blastn [2024-01-25 18:52:46,521] [INFO] Selected 12 target genomes. [2024-01-25 18:52:46,522] [INFO] Target genome list was writen to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt [2024-01-25 18:52:46,523] [INFO] Task started: fastANI [2024-01-25 18:52:46,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17a0182-685a-415d-85fe-362da6566113/GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:53:09,185] [INFO] Task succeeded: fastANI [2024-01-25 18:53:09,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:53:09,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:53:09,194] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold) [2024-01-25 18:53:09,195] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 18:53:09,195] [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 Caballeronia glathei strain=DSM 50014 GCA_000698595.1 60547 60547 type True 100.0 2722 2734 95 conclusive Caballeronia glathei strain=LMG 14190 GCA_000751215.2 60547 60547 type True 99.958 2546 2734 95 conclusive Caballeronia telluris GCA_001544495.2 326475 326475 type True 85.9 1481 2734 95 below_threshold Caballeronia choica GCA_001544535.2 326476 326476 type True 85.8112 1554 2734 95 below_threshold Caballeronia arationis GCA_001544975.2 1777142 1777142 type True 85.7412 1579 2734 95 below_threshold Caballeronia terrestris GCA_001544515.2 1226301 1226301 type True 85.706 1521 2734 95 below_threshold Caballeronia humi GCA_001544475.2 326474 326474 type True 85.4095 1491 2734 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.489 1155 2734 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 81.3185 1022 2734 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 80.9405 1059 2734 95 below_threshold Paraburkholderia silviterrae strain=4M-K11 GCA_004353915.1 2528715 2528715 type True 80.8125 1042 2734 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.6115 1132 2734 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:53:09,196] [INFO] DFAST Taxonomy check result was written to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv [2024-01-25 18:53:09,197] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:53:09,197] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:53:09,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/checkm_data [2024-01-25 18:53:09,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:53:09,277] [INFO] Task started: CheckM [2024-01-25 18:53:09,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/checkm_result [2024-01-25 18:54:19,667] [INFO] Task succeeded: CheckM [2024-01-25 18:54:19,668] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:54:19,692] [INFO] ===== Completeness check finished ===== [2024-01-25 18:54:19,692] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:54:19,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta) [2024-01-25 18:54:19,693] [INFO] Task started: Blastn [2024-01-25 18:54:19,693] [INFO] Running command: blastn -query GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg5788d162-9f8f-43b8-8455-510f643b2651/dqc_reference/reference_markers_gtdb.fasta -out GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:54:21,750] [INFO] Task succeeded: Blastn [2024-01-25 18:54:21,753] [INFO] Selected 6 target genomes. [2024-01-25 18:54:21,753] [INFO] Target genome list was writen to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:54:21,758] [INFO] Task started: fastANI [2024-01-25 18:54:21,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17a0182-685a-415d-85fe-362da6566113/GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:54:34,370] [INFO] Task succeeded: fastANI [2024-01-25 18:54:34,375] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:54:34,375] [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_000698595.1 s__Caballeronia glathei 100.0 2722 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.63 98.92 0.96 0.91 4 conclusive GCF_001544495.1 s__Caballeronia telluris 85.8754 1487 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.07 95.07 0.83 0.83 2 - GCF_001544535.1 s__Caballeronia choica 85.7727 1559 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544975.2 s__Caballeronia arationis 85.7621 1576 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.46 99.46 0.88 0.88 2 - GCF_001544515.1 s__Caballeronia terrestris 85.7131 1520 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_001544475.1 s__Caballeronia humi 85.3718 1496 2734 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.16 95.16 0.85 0.85 2 - -------------------------------------------------------------------------------- [2024-01-25 18:54:34,376] [INFO] GTDB search result was written to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv [2024-01-25 18:54:34,377] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:54:34,380] [INFO] DFAST_QC result json was written to GCF_000698595.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json [2024-01-25 18:54:34,380] [INFO] DFAST_QC completed! [2024-01-25 18:54:34,380] [INFO] Total running time: 0h2m14s