[2024-01-24 12:47:49,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,735] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference
[2024-01-24 12:47:50,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,902] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,902] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7960c0c-1980-4281-ab40-3935d6bdbba7/GCF_001263415.1_ASM126341v1_genomic.fna.gz | prodigal -d GCF_001263415.1_ASM126341v1_genomic.fna/cds.fna -a GCF_001263415.1_ASM126341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:58,303] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:58,304] [INFO] Task started: HMMsearch
[2024-01-24 12:47:58,304] [INFO] Running command: hmmsearch --tblout GCF_001263415.1_ASM126341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/reference_markers.hmm GCF_001263415.1_ASM126341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:58,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:58,578] [INFO] Found 6/6 markers.
[2024-01-24 12:47:58,610] [INFO] Query marker FASTA was written to GCF_001263415.1_ASM126341v1_genomic.fna/markers.fasta
[2024-01-24 12:47:58,611] [INFO] Task started: Blastn
[2024-01-24 12:47:58,611] [INFO] Running command: blastn -query GCF_001263415.1_ASM126341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/reference_markers.fasta -out GCF_001263415.1_ASM126341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:59,198] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:59,203] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:59,204] [INFO] Target genome list was writen to GCF_001263415.1_ASM126341v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:59,268] [INFO] Task started: fastANI
[2024-01-24 12:47:59,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7960c0c-1980-4281-ab40-3935d6bdbba7/GCF_001263415.1_ASM126341v1_genomic.fna.gz --refList GCF_001263415.1_ASM126341v1_genomic.fna/target_genomes.txt --output GCF_001263415.1_ASM126341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:13,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:13,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:13,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:13,223] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:13,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:13,223] [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
Thermincola ferriacetica	strain=Z-0001	GCA_001263415.1	281456	281456	type	True	100.0	1023	1025	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:48:13,225] [INFO] DFAST Taxonomy check result was written to GCF_001263415.1_ASM126341v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:13,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:13,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:13,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/checkm_data
[2024-01-24 12:48:13,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:13,259] [INFO] Task started: CheckM
[2024-01-24 12:48:13,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001263415.1_ASM126341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001263415.1_ASM126341v1_genomic.fna/checkm_input GCF_001263415.1_ASM126341v1_genomic.fna/checkm_result
[2024-01-24 12:48:40,895] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:40,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:40,933] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:40,934] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:40,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001263415.1_ASM126341v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:40,935] [INFO] Task started: Blastn
[2024-01-24 12:48:40,935] [INFO] Running command: blastn -query GCF_001263415.1_ASM126341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcedf1bc-acf1-4af2-9350-e80d8d8879f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001263415.1_ASM126341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:41,782] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:41,786] [INFO] Selected 24 target genomes.
[2024-01-24 12:48:41,787] [INFO] Target genome list was writen to GCF_001263415.1_ASM126341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:41,836] [INFO] Task started: fastANI
[2024-01-24 12:48:41,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7960c0c-1980-4281-ab40-3935d6bdbba7/GCF_001263415.1_ASM126341v1_genomic.fna.gz --refList GCF_001263415.1_ASM126341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001263415.1_ASM126341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:53,322] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:53,325] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:53,325] [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_001263415.1	s__Thermincola ferriacetica	100.0	1023	1025	d__Bacteria;p__Firmicutes_B;c__Thermincolia;o__Thermincolales;f__Thermincolaceae;g__Thermincola	95.0	97.78	97.78	0.87	0.87	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:48:53,327] [INFO] GTDB search result was written to GCF_001263415.1_ASM126341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:53,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:54,092] [INFO] DFAST_QC result json was written to GCF_001263415.1_ASM126341v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:54,092] [INFO] DFAST_QC completed!
[2024-01-24 12:48:54,092] [INFO] Total running time: 0h1m4s