[2024-01-24 13:19:00,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:00,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:00,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference
[2024-01-24 13:19:01,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:01,577] [INFO] Task started: Prodigal
[2024-01-24 13:19:01,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ec22387-0d3b-4449-b6f4-8464708b44a2/GCF_000166095.1_ASM16609v1_genomic.fna.gz | prodigal -d GCF_000166095.1_ASM16609v1_genomic.fna/cds.fna -a GCF_000166095.1_ASM16609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:04,074] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:04,074] [INFO] Task started: HMMsearch
[2024-01-24 13:19:04,075] [INFO] Running command: hmmsearch --tblout GCF_000166095.1_ASM16609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/reference_markers.hmm GCF_000166095.1_ASM16609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:04,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:04,290] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1ec22387-0d3b-4449-b6f4-8464708b44a2/GCF_000166095.1_ASM16609v1_genomic.fna.gz]
[2024-01-24 13:19:04,311] [INFO] Query marker FASTA was written to GCF_000166095.1_ASM16609v1_genomic.fna/markers.fasta
[2024-01-24 13:19:04,311] [INFO] Task started: Blastn
[2024-01-24 13:19:04,311] [INFO] Running command: blastn -query GCF_000166095.1_ASM16609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/reference_markers.fasta -out GCF_000166095.1_ASM16609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,855] [INFO] Selected 4 target genomes.
[2024-01-24 13:19:04,856] [INFO] Target genome list was writen to GCF_000166095.1_ASM16609v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:04,863] [INFO] Task started: fastANI
[2024-01-24 13:19:04,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec22387-0d3b-4449-b6f4-8464708b44a2/GCF_000166095.1_ASM16609v1_genomic.fna.gz --refList GCF_000166095.1_ASM16609v1_genomic.fna/target_genomes.txt --output GCF_000166095.1_ASM16609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:06,356] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:06,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:06,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:06,360] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:06,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:06,360] [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
Methanothermus fervidus	strain=DSM 2088	GCA_000166095.1	2180	2180	type	True	100.0	414	414	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,362] [INFO] DFAST Taxonomy check result was written to GCF_000166095.1_ASM16609v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:06,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:06,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:06,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/checkm_data
[2024-01-24 13:19:06,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:06,377] [INFO] Task started: CheckM
[2024-01-24 13:19:06,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000166095.1_ASM16609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000166095.1_ASM16609v1_genomic.fna/checkm_input GCF_000166095.1_ASM16609v1_genomic.fna/checkm_result
[2024-01-24 13:19:22,936] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:22,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,952] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:22,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:22,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000166095.1_ASM16609v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:22,953] [INFO] Task started: Blastn
[2024-01-24 13:19:22,954] [INFO] Running command: blastn -query GCF_000166095.1_ASM16609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg583866ac-3b59-458f-81a2-d2280e3fac15/dqc_reference/reference_markers_gtdb.fasta -out GCF_000166095.1_ASM16609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:23,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:23,483] [INFO] Selected 6 target genomes.
[2024-01-24 13:19:23,483] [INFO] Target genome list was writen to GCF_000166095.1_ASM16609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:23,520] [INFO] Task started: fastANI
[2024-01-24 13:19:23,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec22387-0d3b-4449-b6f4-8464708b44a2/GCF_000166095.1_ASM16609v1_genomic.fna.gz --refList GCF_000166095.1_ASM16609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000166095.1_ASM16609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:25,889] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,893] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:25,893] [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_000166095.1	s__Methanothermus fervidus	100.0	414	414	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermaceae;g__Methanothermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,895] [INFO] GTDB search result was written to GCF_000166095.1_ASM16609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:25,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:25,898] [INFO] DFAST_QC result json was written to GCF_000166095.1_ASM16609v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:25,898] [INFO] DFAST_QC completed!
[2024-01-24 13:19:25,898] [INFO] Total running time: 0h0m26s