[2024-01-25 19:00:50,749] [INFO] DFAST_QC pipeline started. [2024-01-25 19:00:50,750] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:00:50,750] [INFO] DQC Reference Directory: /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference [2024-01-25 19:00:51,912] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:00:51,913] [INFO] Task started: Prodigal [2024-01-25 19:00:51,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd3834ba-b24c-4bc5-b4c9-9bc28f49dd10/GCF_002895085.1_ASM289508v1_genomic.fna.gz | prodigal -d GCF_002895085.1_ASM289508v1_genomic.fna/cds.fna -a GCF_002895085.1_ASM289508v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:00:53,969] [INFO] Task succeeded: Prodigal [2024-01-25 19:00:53,969] [INFO] Task started: HMMsearch [2024-01-25 19:00:53,969] [INFO] Running command: hmmsearch --tblout GCF_002895085.1_ASM289508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/reference_markers.hmm GCF_002895085.1_ASM289508v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:00:54,165] [INFO] Task succeeded: HMMsearch [2024-01-25 19:00:54,166] [INFO] Found 6/6 markers. [2024-01-25 19:00:54,179] [INFO] Query marker FASTA was written to GCF_002895085.1_ASM289508v1_genomic.fna/markers.fasta [2024-01-25 19:00:54,180] [INFO] Task started: Blastn [2024-01-25 19:00:54,180] [INFO] Running command: blastn -query GCF_002895085.1_ASM289508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/reference_markers.fasta -out GCF_002895085.1_ASM289508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:00:54,727] [INFO] Task succeeded: Blastn [2024-01-25 19:00:54,731] [INFO] Selected 6 target genomes. [2024-01-25 19:00:54,731] [INFO] Target genome list was writen to GCF_002895085.1_ASM289508v1_genomic.fna/target_genomes.txt [2024-01-25 19:00:54,739] [INFO] Task started: fastANI [2024-01-25 19:00:54,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3834ba-b24c-4bc5-b4c9-9bc28f49dd10/GCF_002895085.1_ASM289508v1_genomic.fna.gz --refList GCF_002895085.1_ASM289508v1_genomic.fna/target_genomes.txt --output GCF_002895085.1_ASM289508v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:00:56,337] [INFO] Task succeeded: fastANI [2024-01-25 19:00:56,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:00:56,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:00:56,343] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold) [2024-01-25 19:00:56,343] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:00:56,343] [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 Chlamydia abortus strain=GIMC 2006:CabB577 GCA_002895085.1 83555 83555 type True 100.0 381 381 95 conclusive Chlamydia psittaci strain=6BC GCA_000204255.1 83554 83554 type True 92.9097 369 381 95 below_threshold Chlamydia psittaci strain=6BC GCA_000191925.1 83554 83554 type True 92.899 373 381 95 below_threshold Chlamydia buteonis GCA_900634605.1 2494525 2494525 type True 92.7306 368 381 95 below_threshold Chlamydia poikilotherma strain=S15-834K GCA_900239975.1 1967783 1967783 type True 83.2905 294 381 95 below_threshold Chlamydia caviae GCA_000007605.1 83557 83557 type True 82.86 293 381 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:00:56,345] [INFO] DFAST Taxonomy check result was written to GCF_002895085.1_ASM289508v1_genomic.fna/tc_result.tsv [2024-01-25 19:00:56,345] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:00:56,345] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:00:56,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/checkm_data [2024-01-25 19:00:56,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:00:56,360] [INFO] Task started: CheckM [2024-01-25 19:00:56,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002895085.1_ASM289508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002895085.1_ASM289508v1_genomic.fna/checkm_input GCF_002895085.1_ASM289508v1_genomic.fna/checkm_result [2024-01-25 19:01:09,139] [INFO] Task succeeded: CheckM [2024-01-25 19:01:09,140] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:01:09,158] [INFO] ===== Completeness check finished ===== [2024-01-25 19:01:09,158] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:01:09,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002895085.1_ASM289508v1_genomic.fna/markers.fasta) [2024-01-25 19:01:09,159] [INFO] Task started: Blastn [2024-01-25 19:01:09,159] [INFO] Running command: blastn -query GCF_002895085.1_ASM289508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacaace89-a9c3-4126-9285-965c0f96ffcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002895085.1_ASM289508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:01:10,002] [INFO] Task succeeded: Blastn [2024-01-25 19:01:10,005] [INFO] Selected 7 target genomes. [2024-01-25 19:01:10,005] [INFO] Target genome list was writen to GCF_002895085.1_ASM289508v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:01:10,011] [INFO] Task started: fastANI [2024-01-25 19:01:10,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3834ba-b24c-4bc5-b4c9-9bc28f49dd10/GCF_002895085.1_ASM289508v1_genomic.fna.gz --refList GCF_002895085.1_ASM289508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002895085.1_ASM289508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:01:11,936] [INFO] Task succeeded: fastANI [2024-01-25 19:01:11,941] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:01:11,942] [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_002895085.1 s__Chlamydophila abortus 100.0 381 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.82 97.53 0.99 0.97 57 conclusive GCF_000204255.1 s__Chlamydophila psittaci 92.9097 369 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.65 97.64 1.00 0.97 66 - GCF_900634605.1 s__Chlamydophila buteonis 92.7306 368 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 99.99 99.99 1.00 1.00 3 - GCF_900239975.1 s__Chlamydophila sp900239975 83.313 293 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_018343815.1 s__Chlamydophila sp018343815 83.002 318 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000007605.1 s__Chlamydophila caviae 82.86 293 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - GCF_000009945.1 s__Chlamydophila felis 82.4044 300 381 d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 19:01:11,943] [INFO] GTDB search result was written to GCF_002895085.1_ASM289508v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:01:11,943] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:01:11,945] [INFO] DFAST_QC result json was written to GCF_002895085.1_ASM289508v1_genomic.fna/dqc_result.json [2024-01-25 19:01:11,945] [INFO] DFAST_QC completed! [2024-01-25 19:01:11,945] [INFO] Total running time: 0h0m21s