[2024-01-24 13:13:39,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference
[2024-01-24 13:13:40,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,530] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg07428f4b-6201-41f4-8323-23b50ee45108/GCF_028472365.1_ASM2847236v1_genomic.fna.gz | prodigal -d GCF_028472365.1_ASM2847236v1_genomic.fna/cds.fna -a GCF_028472365.1_ASM2847236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:47,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:47,918] [INFO] Task started: HMMsearch
[2024-01-24 13:13:47,918] [INFO] Running command: hmmsearch --tblout GCF_028472365.1_ASM2847236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/reference_markers.hmm GCF_028472365.1_ASM2847236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:48,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:48,180] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg07428f4b-6201-41f4-8323-23b50ee45108/GCF_028472365.1_ASM2847236v1_genomic.fna.gz]
[2024-01-24 13:13:48,206] [INFO] Query marker FASTA was written to GCF_028472365.1_ASM2847236v1_genomic.fna/markers.fasta
[2024-01-24 13:13:48,206] [INFO] Task started: Blastn
[2024-01-24 13:13:48,206] [INFO] Running command: blastn -query GCF_028472365.1_ASM2847236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/reference_markers.fasta -out GCF_028472365.1_ASM2847236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:48,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:48,675] [INFO] Selected 1 target genomes.
[2024-01-24 13:13:48,675] [INFO] Target genome list was writen to GCF_028472365.1_ASM2847236v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:48,676] [INFO] Task started: fastANI
[2024-01-24 13:13:48,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg07428f4b-6201-41f4-8323-23b50ee45108/GCF_028472365.1_ASM2847236v1_genomic.fna.gz --refList GCF_028472365.1_ASM2847236v1_genomic.fna/target_genomes.txt --output GCF_028472365.1_ASM2847236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:49,520] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:49,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:49,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:49,524] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:49,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:49,524] [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
Sulfolobus acidocaldarius	strain=DSM 639	GCA_000012285.1	2285	2285	type	True	99.9947	740	741	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:13:49,526] [INFO] DFAST Taxonomy check result was written to GCF_028472365.1_ASM2847236v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:49,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:49,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:49,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/checkm_data
[2024-01-24 13:13:49,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:49,552] [INFO] Task started: CheckM
[2024-01-24 13:13:49,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028472365.1_ASM2847236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028472365.1_ASM2847236v1_genomic.fna/checkm_input GCF_028472365.1_ASM2847236v1_genomic.fna/checkm_result
[2024-01-24 13:14:16,256] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:16,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:16,274] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:16,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:16,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028472365.1_ASM2847236v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:16,275] [INFO] Task started: Blastn
[2024-01-24 13:14:16,275] [INFO] Running command: blastn -query GCF_028472365.1_ASM2847236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ae6890-ffeb-4301-b243-dc4790ee059a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028472365.1_ASM2847236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:16,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:16,705] [INFO] Selected 3 target genomes.
[2024-01-24 13:14:16,705] [INFO] Target genome list was writen to GCF_028472365.1_ASM2847236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:16,708] [INFO] Task started: fastANI
[2024-01-24 13:14:16,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg07428f4b-6201-41f4-8323-23b50ee45108/GCF_028472365.1_ASM2847236v1_genomic.fna.gz --refList GCF_028472365.1_ASM2847236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028472365.1_ASM2847236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:18,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,386] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:18,387] [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_000012285.1	s__Sulfolobus acidocaldarius	99.9947	740	741	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus	95.0	99.98	99.96	0.99	0.97	56	conclusive
GCA_000508305.1	s__Sulfolobus acidocaldarius_A	93.6216	630	741	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,389] [INFO] GTDB search result was written to GCF_028472365.1_ASM2847236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:18,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:18,392] [INFO] DFAST_QC result json was written to GCF_028472365.1_ASM2847236v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:18,392] [INFO] DFAST_QC completed!
[2024-01-24 13:14:18,393] [INFO] Total running time: 0h0m39s