[2024-01-24 14:22:32,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:32,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:32,835] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference
[2024-01-24 14:22:34,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,125] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c2a337c-2426-498e-b603-14caa5329236/GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/cds.fna -a GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,069] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,070] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,070] [INFO] Running command: hmmsearch --tblout GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/reference_markers.hmm GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:45,334] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:45,335] [INFO] Found 6/6 markers.
[2024-01-24 14:22:45,369] [INFO] Query marker FASTA was written to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:45,370] [INFO] Task started: Blastn
[2024-01-24 14:22:45,370] [INFO] Running command: blastn -query GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/reference_markers.fasta -out GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:46,046] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:46,050] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:46,051] [INFO] Target genome list was writen to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:46,063] [INFO] Task started: fastANI
[2024-01-24 14:22:46,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c2a337c-2426-498e-b603-14caa5329236/GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna.gz --refList GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:55,094] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:55,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:55,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:55,102] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:55,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:55,102] [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
Sulfobacillus thermosulfidooxidans	strain=DSM 9293	GCA_900176145.1	28034	28034	type	True	100.0	1286	1286	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,104] [INFO] DFAST Taxonomy check result was written to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:22:55,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:55,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:55,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/checkm_data
[2024-01-24 14:22:55,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:55,149] [INFO] Task started: CheckM
[2024-01-24 14:22:55,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/checkm_input GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:23:32,294] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:32,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:32,326] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:32,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:32,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:23:32,327] [INFO] Task started: Blastn
[2024-01-24 14:23:32,327] [INFO] Running command: blastn -query GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf413add-1eb2-4e11-815b-23079d0dae72/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:33,200] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:33,204] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:33,205] [INFO] Target genome list was writen to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:33,240] [INFO] Task started: fastANI
[2024-01-24 14:23:33,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c2a337c-2426-498e-b603-14caa5329236/GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna.gz --refList GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:40,666] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:40,674] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:40,674] [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_900176145.1	s__Sulfobacillus thermosulfidooxidans	100.0	1286	1286	d__Bacteria;p__Firmicutes_E;c__Sulfobacillia;o__Sulfobacillales;f__Sulfobacillaceae;g__Sulfobacillus	95.0	97.62	97.10	0.92	0.87	7	conclusive
GCF_001280565.1	s__Sulfobacillus thermosulfidooxidans_A	87.6087	959	1286	d__Bacteria;p__Firmicutes_E;c__Sulfobacillia;o__Sulfobacillales;f__Sulfobacillaceae;g__Sulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023725.1	s__Sulfobacillus benefaciens_A	77.8668	182	1286	d__Bacteria;p__Firmicutes_E;c__Sulfobacillia;o__Sulfobacillales;f__Sulfobacillaceae;g__Sulfobacillus	95.0	99.29	99.29	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:40,676] [INFO] GTDB search result was written to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:40,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:40,680] [INFO] DFAST_QC result json was written to GCF_900176145.1_IMG-taxon_2506210005_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:23:40,680] [INFO] DFAST_QC completed!
[2024-01-24 14:23:40,680] [INFO] Total running time: 0h1m8s