[2024-01-24 15:27:41,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference
[2024-01-24 15:27:43,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,886] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a8b9f6f-676a-4828-aecb-7edf1ae173ee/GCF_001006045.1_ASM100604v1_genomic.fna.gz | prodigal -d GCF_001006045.1_ASM100604v1_genomic.fna/cds.fna -a GCF_001006045.1_ASM100604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:52,676] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:52,677] [INFO] Task started: HMMsearch
[2024-01-24 15:27:52,677] [INFO] Running command: hmmsearch --tblout GCF_001006045.1_ASM100604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/reference_markers.hmm GCF_001006045.1_ASM100604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:52,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:52,924] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1a8b9f6f-676a-4828-aecb-7edf1ae173ee/GCF_001006045.1_ASM100604v1_genomic.fna.gz]
[2024-01-24 15:27:52,942] [INFO] Query marker FASTA was written to GCF_001006045.1_ASM100604v1_genomic.fna/markers.fasta
[2024-01-24 15:27:52,943] [INFO] Task started: Blastn
[2024-01-24 15:27:52,943] [INFO] Running command: blastn -query GCF_001006045.1_ASM100604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/reference_markers.fasta -out GCF_001006045.1_ASM100604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:53,426] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:53,429] [INFO] Selected 5 target genomes.
[2024-01-24 15:27:53,430] [INFO] Target genome list was writen to GCF_001006045.1_ASM100604v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:53,470] [INFO] Task started: fastANI
[2024-01-24 15:27:53,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a8b9f6f-676a-4828-aecb-7edf1ae173ee/GCF_001006045.1_ASM100604v1_genomic.fna.gz --refList GCF_001006045.1_ASM100604v1_genomic.fna/target_genomes.txt --output GCF_001006045.1_ASM100604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:57,752] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:57,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:57,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:57,759] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:57,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:57,760] [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
Geoglobus ahangari	strain=234	GCA_001006045.1	113653	113653	type	True	100.0	590	590	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:27:57,762] [INFO] DFAST Taxonomy check result was written to GCF_001006045.1_ASM100604v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:57,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:57,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:57,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/checkm_data
[2024-01-24 15:27:57,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:57,789] [INFO] Task started: CheckM
[2024-01-24 15:27:57,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001006045.1_ASM100604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001006045.1_ASM100604v1_genomic.fna/checkm_input GCF_001006045.1_ASM100604v1_genomic.fna/checkm_result
[2024-01-24 15:28:28,473] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:28,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:28,496] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:28,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:28,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001006045.1_ASM100604v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:28,497] [INFO] Task started: Blastn
[2024-01-24 15:28:28,497] [INFO] Running command: blastn -query GCF_001006045.1_ASM100604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd6698f-c60a-4d27-8be1-c1a35c60deb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001006045.1_ASM100604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:28,941] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:28,945] [INFO] Selected 9 target genomes.
[2024-01-24 15:28:28,945] [INFO] Target genome list was writen to GCF_001006045.1_ASM100604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:28,958] [INFO] Task started: fastANI
[2024-01-24 15:28:28,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a8b9f6f-676a-4828-aecb-7edf1ae173ee/GCF_001006045.1_ASM100604v1_genomic.fna.gz --refList GCF_001006045.1_ASM100604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001006045.1_ASM100604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:32,191] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:32,196] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:32,196] [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_001006045.1	s__Geoglobus ahangari	100.0	590	590	d__Archaea;p__Halobacteriota;c__Archaeoglobi;o__Archaeoglobales;f__Archaeoglobaceae;g__Geoglobus	95.0	97.56	97.56	0.99	0.99	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:28:32,294] [INFO] GTDB search result was written to GCF_001006045.1_ASM100604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:32,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:32,298] [INFO] DFAST_QC result json was written to GCF_001006045.1_ASM100604v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:32,298] [INFO] DFAST_QC completed!
[2024-01-24 15:28:32,298] [INFO] Total running time: 0h0m51s