[2024-01-25 17:53:50,822] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference
[2024-01-25 17:53:52,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:52,011] [INFO] Task started: Prodigal
[2024-01-25 17:53:52,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg45ff8f2b-169a-41ec-890d-a32dec44df66/GCF_002369955.1_ASM236995v1_genomic.fna.gz | prodigal -d GCF_002369955.1_ASM236995v1_genomic.fna/cds.fna -a GCF_002369955.1_ASM236995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:56,933] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:56,933] [INFO] Task started: HMMsearch
[2024-01-25 17:53:56,933] [INFO] Running command: hmmsearch --tblout GCF_002369955.1_ASM236995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/reference_markers.hmm GCF_002369955.1_ASM236995v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:57,112] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:57,113] [INFO] Found 6/6 markers.
[2024-01-25 17:53:57,130] [INFO] Query marker FASTA was written to GCF_002369955.1_ASM236995v1_genomic.fna/markers.fasta
[2024-01-25 17:53:57,130] [INFO] Task started: Blastn
[2024-01-25 17:53:57,130] [INFO] Running command: blastn -query GCF_002369955.1_ASM236995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/reference_markers.fasta -out GCF_002369955.1_ASM236995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:57,687] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:57,690] [INFO] Selected 19 target genomes.
[2024-01-25 17:53:57,690] [INFO] Target genome list was writen to GCF_002369955.1_ASM236995v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:57,707] [INFO] Task started: fastANI
[2024-01-25 17:53:57,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg45ff8f2b-169a-41ec-890d-a32dec44df66/GCF_002369955.1_ASM236995v1_genomic.fna.gz --refList GCF_002369955.1_ASM236995v1_genomic.fna/target_genomes.txt --output GCF_002369955.1_ASM236995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:10,354] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:10,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:10,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:10,358] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:10,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:10,358] [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
Ichthyobacterium seriolicida	strain=JBKA-6	GCA_002369955.1	242600	242600	type	True	100.0	640	640	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:54:10,359] [INFO] DFAST Taxonomy check result was written to GCF_002369955.1_ASM236995v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:10,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:10,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:10,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/checkm_data
[2024-01-25 17:54:10,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:10,382] [INFO] Task started: CheckM
[2024-01-25 17:54:10,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002369955.1_ASM236995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002369955.1_ASM236995v1_genomic.fna/checkm_input GCF_002369955.1_ASM236995v1_genomic.fna/checkm_result
[2024-01-25 17:54:29,760] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:29,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:29,774] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:29,774] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:29,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002369955.1_ASM236995v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:29,774] [INFO] Task started: Blastn
[2024-01-25 17:54:29,774] [INFO] Running command: blastn -query GCF_002369955.1_ASM236995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5cfe83-1f40-45b7-91b7-7adbb4e48646/dqc_reference/reference_markers_gtdb.fasta -out GCF_002369955.1_ASM236995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:30,707] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:30,710] [INFO] Selected 29 target genomes.
[2024-01-25 17:54:30,710] [INFO] Target genome list was writen to GCF_002369955.1_ASM236995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:30,737] [INFO] Task started: fastANI
[2024-01-25 17:54:30,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg45ff8f2b-169a-41ec-890d-a32dec44df66/GCF_002369955.1_ASM236995v1_genomic.fna.gz --refList GCF_002369955.1_ASM236995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002369955.1_ASM236995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:45,453] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:45,455] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:45,455] [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_002369955.1	s__Ichthyobacterium seriolicida	100.0	640	640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Ichthyobacteriaceae;g__Ichthyobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:54:45,457] [INFO] GTDB search result was written to GCF_002369955.1_ASM236995v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:45,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:45,459] [INFO] DFAST_QC result json was written to GCF_002369955.1_ASM236995v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:45,459] [INFO] DFAST_QC completed!
[2024-01-25 17:54:45,459] [INFO] Total running time: 0h0m55s