[2024-01-24 12:31:58,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference
[2024-01-24 12:31:59,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,802] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,802] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf590a68-4c61-4ce6-904b-efcc012117a2/GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/cds.fna -a GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:06,489] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:06,490] [INFO] Task started: HMMsearch
[2024-01-24 12:32:06,490] [INFO] Running command: hmmsearch --tblout GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/reference_markers.hmm GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:06,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:06,758] [INFO] Found 6/6 markers.
[2024-01-24 12:32:06,784] [INFO] Query marker FASTA was written to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:06,785] [INFO] Task started: Blastn
[2024-01-24 12:32:06,785] [INFO] Running command: blastn -query GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/reference_markers.fasta -out GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:07,468] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:07,472] [INFO] Selected 29 target genomes.
[2024-01-24 12:32:07,473] [INFO] Target genome list was writen to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:07,488] [INFO] Task started: fastANI
[2024-01-24 12:32:07,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf590a68-4c61-4ce6-904b-efcc012117a2/GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna.gz --refList GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:23,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:23,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:23,894] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:23,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:23,894] [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
Pilibacter termitis	strain=ATCC BAA-1030	GCA_900167335.1	263852	263852	type	True	100.0	892	898	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,896] [INFO] DFAST Taxonomy check result was written to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:23,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:23,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:23,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/checkm_data
[2024-01-24 12:32:23,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:23,928] [INFO] Task started: CheckM
[2024-01-24 12:32:23,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/checkm_input GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:51,361] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:51,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:51,382] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:51,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:51,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:51,383] [INFO] Task started: Blastn
[2024-01-24 12:32:51,383] [INFO] Running command: blastn -query GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg14f77396-9b14-4307-b504-e2354d60dcc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:52,112] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:52,117] [INFO] Selected 28 target genomes.
[2024-01-24 12:32:52,118] [INFO] Target genome list was writen to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:52,142] [INFO] Task started: fastANI
[2024-01-24 12:32:52,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf590a68-4c61-4ce6-904b-efcc012117a2/GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna.gz --refList GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:07,195] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:07,198] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:07,199] [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_900167335.1	s__Pilibacter termitis	100.0	892	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Pilibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:33:07,200] [INFO] GTDB search result was written to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:07,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:07,203] [INFO] DFAST_QC result json was written to GCF_900167335.1_IMG-taxon_2585428141_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:33:07,204] [INFO] DFAST_QC completed!
[2024-01-24 12:33:07,204] [INFO] Total running time: 0h1m9s