[2024-01-25 17:45:50,611] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:50,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:50,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference
[2024-01-25 17:45:51,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:51,715] [INFO] Task started: Prodigal
[2024-01-25 17:45:51,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eebd545-262e-42d4-9c50-b23c48ed8e28/GCF_009910365.1_ASM991036v1_genomic.fna.gz | prodigal -d GCF_009910365.1_ASM991036v1_genomic.fna/cds.fna -a GCF_009910365.1_ASM991036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:59,317] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:59,317] [INFO] Task started: HMMsearch
[2024-01-25 17:45:59,317] [INFO] Running command: hmmsearch --tblout GCF_009910365.1_ASM991036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/reference_markers.hmm GCF_009910365.1_ASM991036v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:59,540] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:59,541] [INFO] Found 6/6 markers.
[2024-01-25 17:45:59,568] [INFO] Query marker FASTA was written to GCF_009910365.1_ASM991036v1_genomic.fna/markers.fasta
[2024-01-25 17:45:59,568] [INFO] Task started: Blastn
[2024-01-25 17:45:59,568] [INFO] Running command: blastn -query GCF_009910365.1_ASM991036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/reference_markers.fasta -out GCF_009910365.1_ASM991036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:00,211] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:00,213] [INFO] Selected 24 target genomes.
[2024-01-25 17:46:00,214] [INFO] Target genome list was writen to GCF_009910365.1_ASM991036v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:00,238] [INFO] Task started: fastANI
[2024-01-25 17:46:00,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eebd545-262e-42d4-9c50-b23c48ed8e28/GCF_009910365.1_ASM991036v1_genomic.fna.gz --refList GCF_009910365.1_ASM991036v1_genomic.fna/target_genomes.txt --output GCF_009910365.1_ASM991036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:16,421] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:16,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:16,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:16,425] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:46:16,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:16,426] [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
Aequoribacter fuscus	strain=IMCC3088	GCA_009910365.1	2518989	2518989	type	True	100.0	1030	1031	95	conclusive
Aequoribacter fuscus	strain=IMCC3088	GCA_000204315.2	2518989	2518989	type	True	99.8841	924	1031	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:46:16,427] [INFO] DFAST Taxonomy check result was written to GCF_009910365.1_ASM991036v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:16,427] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:16,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:16,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/checkm_data
[2024-01-25 17:46:16,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:16,463] [INFO] Task started: CheckM
[2024-01-25 17:46:16,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009910365.1_ASM991036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009910365.1_ASM991036v1_genomic.fna/checkm_input GCF_009910365.1_ASM991036v1_genomic.fna/checkm_result
[2024-01-25 17:46:42,566] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:42,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:42,588] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:42,588] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:42,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009910365.1_ASM991036v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:42,589] [INFO] Task started: Blastn
[2024-01-25 17:46:42,589] [INFO] Running command: blastn -query GCF_009910365.1_ASM991036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3a0c02-9a4d-4577-b2e1-5743486b404f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009910365.1_ASM991036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:43,742] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:43,745] [INFO] Selected 29 target genomes.
[2024-01-25 17:46:43,746] [INFO] Target genome list was writen to GCF_009910365.1_ASM991036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:43,775] [INFO] Task started: fastANI
[2024-01-25 17:46:43,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eebd545-262e-42d4-9c50-b23c48ed8e28/GCF_009910365.1_ASM991036v1_genomic.fna.gz --refList GCF_009910365.1_ASM991036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009910365.1_ASM991036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:00,586] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:00,589] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:00,589] [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_009910365.1	s__Aequoribacter fuscus	100.0	1027	1031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Aequoribacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:47:00,591] [INFO] GTDB search result was written to GCF_009910365.1_ASM991036v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:00,592] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:00,593] [INFO] DFAST_QC result json was written to GCF_009910365.1_ASM991036v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:00,594] [INFO] DFAST_QC completed!
[2024-01-25 17:47:00,594] [INFO] Total running time: 0h1m10s