[2024-01-24 13:01:53,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference
[2024-01-24 13:01:54,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,670] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg24ae2c4f-23c5-464d-aa75-3b3b392bc15a/GCF_009729515.1_ASM972951v1_genomic.fna.gz | prodigal -d GCF_009729515.1_ASM972951v1_genomic.fna/cds.fna -a GCF_009729515.1_ASM972951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:02,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:02,552] [INFO] Task started: HMMsearch
[2024-01-24 13:02:02,552] [INFO] Running command: hmmsearch --tblout GCF_009729515.1_ASM972951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/reference_markers.hmm GCF_009729515.1_ASM972951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:02,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:02,786] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg24ae2c4f-23c5-464d-aa75-3b3b392bc15a/GCF_009729515.1_ASM972951v1_genomic.fna.gz]
[2024-01-24 13:02:02,820] [INFO] Query marker FASTA was written to GCF_009729515.1_ASM972951v1_genomic.fna/markers.fasta
[2024-01-24 13:02:02,821] [INFO] Task started: Blastn
[2024-01-24 13:02:02,821] [INFO] Running command: blastn -query GCF_009729515.1_ASM972951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/reference_markers.fasta -out GCF_009729515.1_ASM972951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:03,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:03,385] [INFO] Selected 3 target genomes.
[2024-01-24 13:02:03,385] [INFO] Target genome list was writen to GCF_009729515.1_ASM972951v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:03,401] [INFO] Task started: fastANI
[2024-01-24 13:02:03,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg24ae2c4f-23c5-464d-aa75-3b3b392bc15a/GCF_009729515.1_ASM972951v1_genomic.fna.gz --refList GCF_009729515.1_ASM972951v1_genomic.fna/target_genomes.txt --output GCF_009729515.1_ASM972951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:05,619] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:05,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:05,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:05,625] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:05,625] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:05,625] [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
Sulfuracidifex metallicus	strain=DSM 6482	GCA_009729515.1	47303	47303	type	True	100.0	735	735	95	conclusive
Sulfuracidifex metallicus	strain=JCM 9184	GCA_001316045.1	47303	47303	type	True	99.6707	658	735	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:02:05,627] [INFO] DFAST Taxonomy check result was written to GCF_009729515.1_ASM972951v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:05,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:05,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:05,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/checkm_data
[2024-01-24 13:02:05,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:05,653] [INFO] Task started: CheckM
[2024-01-24 13:02:05,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009729515.1_ASM972951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009729515.1_ASM972951v1_genomic.fna/checkm_input GCF_009729515.1_ASM972951v1_genomic.fna/checkm_result
[2024-01-24 13:02:35,137] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:35,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:35,161] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:35,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:35,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009729515.1_ASM972951v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:35,162] [INFO] Task started: Blastn
[2024-01-24 13:02:35,163] [INFO] Running command: blastn -query GCF_009729515.1_ASM972951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e1f05ab-3856-4b45-be21-6b11936bd6e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009729515.1_ASM972951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:35,577] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:35,581] [INFO] Selected 2 target genomes.
[2024-01-24 13:02:35,581] [INFO] Target genome list was writen to GCF_009729515.1_ASM972951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:35,584] [INFO] Task started: fastANI
[2024-01-24 13:02:35,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg24ae2c4f-23c5-464d-aa75-3b3b392bc15a/GCF_009729515.1_ASM972951v1_genomic.fna.gz --refList GCF_009729515.1_ASM972951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009729515.1_ASM972951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:36,583] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:36,588] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:36,588] [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
--------------------------------------------------------------------------------
[2024-01-24 13:02:36,590] [INFO] GTDB search result was written to GCF_009729515.1_ASM972951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:36,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:36,592] [INFO] DFAST_QC result json was written to GCF_009729515.1_ASM972951v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:36,593] [INFO] DFAST_QC completed!
[2024-01-24 13:02:36,593] [INFO] Total running time: 0h0m43s