[2024-01-24 14:06:06,272] [INFO] DFAST_QC pipeline started. [2024-01-24 14:06:06,274] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:06:06,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference [2024-01-24 14:06:07,638] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:06:07,639] [INFO] Task started: Prodigal [2024-01-24 14:06:07,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a84dbf3-a29a-4af7-9720-ab77dc0a211d/GCF_000751215.2_Bglat_v2_genomic.fna.gz | prodigal -d GCF_000751215.2_Bglat_v2_genomic.fna/cds.fna -a GCF_000751215.2_Bglat_v2_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:06:32,230] [INFO] Task succeeded: Prodigal [2024-01-24 14:06:32,231] [INFO] Task started: HMMsearch [2024-01-24 14:06:32,231] [INFO] Running command: hmmsearch --tblout GCF_000751215.2_Bglat_v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/reference_markers.hmm GCF_000751215.2_Bglat_v2_genomic.fna/protein.faa > /dev/null [2024-01-24 14:06:32,703] [INFO] Task succeeded: HMMsearch [2024-01-24 14:06:32,705] [INFO] Found 6/6 markers. [2024-01-24 14:06:32,771] [INFO] Query marker FASTA was written to GCF_000751215.2_Bglat_v2_genomic.fna/markers.fasta [2024-01-24 14:06:32,772] [INFO] Task started: Blastn [2024-01-24 14:06:32,772] [INFO] Running command: blastn -query GCF_000751215.2_Bglat_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/reference_markers.fasta -out GCF_000751215.2_Bglat_v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:06:33,797] [INFO] Task succeeded: Blastn [2024-01-24 14:06:33,801] [INFO] Selected 12 target genomes. [2024-01-24 14:06:33,802] [INFO] Target genome list was writen to GCF_000751215.2_Bglat_v2_genomic.fna/target_genomes.txt [2024-01-24 14:06:33,807] [INFO] Task started: fastANI [2024-01-24 14:06:33,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a84dbf3-a29a-4af7-9720-ab77dc0a211d/GCF_000751215.2_Bglat_v2_genomic.fna.gz --refList GCF_000751215.2_Bglat_v2_genomic.fna/target_genomes.txt --output GCF_000751215.2_Bglat_v2_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:06:56,894] [INFO] Task succeeded: fastANI [2024-01-24 14:06:56,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:06:56,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:06:56,905] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold) [2024-01-24 14:06:56,905] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:06:56,905] [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=LMG 14190 GCA_000751215.2 60547 60547 type True 100.0 2609 2618 95 conclusive Caballeronia glathei strain=DSM 50014 GCA_000698595.1 60547 60547 type True 99.9674 2516 2618 95 conclusive Caballeronia telluris GCA_001544495.2 326475 326475 type True 86.0456 1459 2618 95 below_threshold Caballeronia choica GCA_001544535.2 326476 326476 type True 85.8523 1533 2618 95 below_threshold Caballeronia arationis GCA_001544975.2 1777142 1777142 type True 85.7297 1568 2618 95 below_threshold Caballeronia terrestris GCA_001544515.2 1226301 1226301 type True 85.5887 1510 2618 95 below_threshold Caballeronia humi GCA_001544475.2 326474 326474 type True 85.544 1478 2618 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 81.6017 1149 2618 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 81.5265 1026 2618 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 81.1456 1069 2618 95 below_threshold Paraburkholderia silviterrae strain=4M-K11 GCA_004353915.1 2528715 2528715 type True 80.8357 1052 2618 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 80.8053 1123 2618 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:06:56,907] [INFO] DFAST Taxonomy check result was written to GCF_000751215.2_Bglat_v2_genomic.fna/tc_result.tsv [2024-01-24 14:06:56,908] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:06:56,908] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:06:56,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/checkm_data [2024-01-24 14:06:56,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:06:56,988] [INFO] Task started: CheckM [2024-01-24 14:06:56,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000751215.2_Bglat_v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000751215.2_Bglat_v2_genomic.fna/checkm_input GCF_000751215.2_Bglat_v2_genomic.fna/checkm_result [2024-01-24 14:08:09,013] [INFO] Task succeeded: CheckM [2024-01-24 14:08:09,014] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:08:09,039] [INFO] ===== Completeness check finished ===== [2024-01-24 14:08:09,039] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:08:09,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000751215.2_Bglat_v2_genomic.fna/markers.fasta) [2024-01-24 14:08:09,040] [INFO] Task started: Blastn [2024-01-24 14:08:09,040] [INFO] Running command: blastn -query GCF_000751215.2_Bglat_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a9ebaaf-bf8e-4627-8610-4c3f97cb9ae7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000751215.2_Bglat_v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:08:11,042] [INFO] Task succeeded: Blastn [2024-01-24 14:08:11,046] [INFO] Selected 6 target genomes. [2024-01-24 14:08:11,046] [INFO] Target genome list was writen to GCF_000751215.2_Bglat_v2_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:08:11,058] [INFO] Task started: fastANI [2024-01-24 14:08:11,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a84dbf3-a29a-4af7-9720-ab77dc0a211d/GCF_000751215.2_Bglat_v2_genomic.fna.gz --refList GCF_000751215.2_Bglat_v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000751215.2_Bglat_v2_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:08:23,470] [INFO] Task succeeded: fastANI [2024-01-24 14:08:23,483] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:08:23,483] [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 99.9674 2516 2618 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 86.0303 1460 2618 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 85.8459 1535 2618 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 85.7099 1571 2618 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 85.5695 1513 2618 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 85.5441 1478 2618 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 95.16 95.16 0.85 0.85 2 - -------------------------------------------------------------------------------- [2024-01-24 14:08:23,485] [INFO] GTDB search result was written to GCF_000751215.2_Bglat_v2_genomic.fna/result_gtdb.tsv [2024-01-24 14:08:23,485] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:08:23,488] [INFO] DFAST_QC result json was written to GCF_000751215.2_Bglat_v2_genomic.fna/dqc_result.json [2024-01-24 14:08:23,488] [INFO] DFAST_QC completed! [2024-01-24 14:08:23,488] [INFO] Total running time: 0h2m17s