[2024-01-24 13:46:43,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:43,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:43,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference
[2024-01-24 13:46:45,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:45,298] [INFO] Task started: Prodigal
[2024-01-24 13:46:45,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg741a0849-96ca-49cf-82de-9940f6b2cbfb/GCF_003201835.2_ASM320183v2_genomic.fna.gz | prodigal -d GCF_003201835.2_ASM320183v2_genomic.fna/cds.fna -a GCF_003201835.2_ASM320183v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:53,224] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:53,224] [INFO] Task started: HMMsearch
[2024-01-24 13:46:53,224] [INFO] Running command: hmmsearch --tblout GCF_003201835.2_ASM320183v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/reference_markers.hmm GCF_003201835.2_ASM320183v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:53,467] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:53,468] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg741a0849-96ca-49cf-82de-9940f6b2cbfb/GCF_003201835.2_ASM320183v2_genomic.fna.gz]
[2024-01-24 13:46:53,497] [INFO] Query marker FASTA was written to GCF_003201835.2_ASM320183v2_genomic.fna/markers.fasta
[2024-01-24 13:46:53,498] [INFO] Task started: Blastn
[2024-01-24 13:46:53,498] [INFO] Running command: blastn -query GCF_003201835.2_ASM320183v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/reference_markers.fasta -out GCF_003201835.2_ASM320183v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:53,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:54,003] [INFO] Selected 2 target genomes.
[2024-01-24 13:46:54,003] [INFO] Target genome list was writen to GCF_003201835.2_ASM320183v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:54,006] [INFO] Task started: fastANI
[2024-01-24 13:46:54,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg741a0849-96ca-49cf-82de-9940f6b2cbfb/GCF_003201835.2_ASM320183v2_genomic.fna.gz --refList GCF_003201835.2_ASM320183v2_genomic.fna/target_genomes.txt --output GCF_003201835.2_ASM320183v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:57,231] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:57,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:57,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:57,239] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:57,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:57,239] [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
Acidianus brierleyi	strain=DSM 1651	GCA_003201835.2	41673	41673	type	True	100.0	982	982	95	conclusive
Sulfuracidifex metallicus	strain=DSM 6482	GCA_009729515.1	47303	47303	type	True	77.7934	51	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,242] [INFO] DFAST Taxonomy check result was written to GCF_003201835.2_ASM320183v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:57,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:57,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:57,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/checkm_data
[2024-01-24 13:46:57,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:57,288] [INFO] Task started: CheckM
[2024-01-24 13:46:57,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201835.2_ASM320183v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201835.2_ASM320183v2_genomic.fna/checkm_input GCF_003201835.2_ASM320183v2_genomic.fna/checkm_result
[2024-01-24 13:47:26,357] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:26,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:26,381] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:26,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:26,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201835.2_ASM320183v2_genomic.fna/markers.fasta)
[2024-01-24 13:47:26,382] [INFO] Task started: Blastn
[2024-01-24 13:47:26,382] [INFO] Running command: blastn -query GCF_003201835.2_ASM320183v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a805619-6698-443c-8acd-68d2921e57c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201835.2_ASM320183v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:26,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:26,833] [INFO] Selected 4 target genomes.
[2024-01-24 13:47:26,833] [INFO] Target genome list was writen to GCF_003201835.2_ASM320183v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:26,856] [INFO] Task started: fastANI
[2024-01-24 13:47:26,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg741a0849-96ca-49cf-82de-9940f6b2cbfb/GCF_003201835.2_ASM320183v2_genomic.fna.gz --refList GCF_003201835.2_ASM320183v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003201835.2_ASM320183v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:30,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:30,355] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:30,355] [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_003201835.2	s__Acidianus_B brierleyi	100.0	982	982	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Acidianus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003086435.1	s__Acidianus hospitalis	79.8528	104	982	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Acidianus	95.0	97.25	97.25	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,357] [INFO] GTDB search result was written to GCF_003201835.2_ASM320183v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:30,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:30,360] [INFO] DFAST_QC result json was written to GCF_003201835.2_ASM320183v2_genomic.fna/dqc_result.json
[2024-01-24 13:47:30,360] [INFO] DFAST_QC completed!
[2024-01-24 13:47:30,360] [INFO] Total running time: 0h0m46s