[2024-01-24 13:33:10,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:10,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:10,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference
[2024-01-24 13:33:12,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,085] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb38c8a1-fa9a-4204-bf1e-c87d81d5d481/GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/cds.fna -a GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:37,383] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:37,384] [INFO] Task started: HMMsearch
[2024-01-24 13:33:37,384] [INFO] Running command: hmmsearch --tblout GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/reference_markers.hmm GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:37,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:37,681] [INFO] Found 6/6 markers.
[2024-01-24 13:33:37,718] [INFO] Query marker FASTA was written to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:33:37,719] [INFO] Task started: Blastn
[2024-01-24 13:33:37,719] [INFO] Running command: blastn -query GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/reference_markers.fasta -out GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:38,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:38,338] [INFO] Selected 33 target genomes.
[2024-01-24 13:33:38,339] [INFO] Target genome list was writen to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:33:38,363] [INFO] Task started: fastANI
[2024-01-24 13:33:38,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb38c8a1-fa9a-4204-bf1e-c87d81d5d481/GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna.gz --refList GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:05,502] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:05,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:05,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:05,510] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:34:05,510] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:05,510] [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
Flexibacter flexilis	strain=DSM 6793	GCA_900112255.1	998	998	type	True	100.0	1391	1393	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:34:05,512] [INFO] DFAST Taxonomy check result was written to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:34:05,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:05,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:05,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/checkm_data
[2024-01-24 13:34:05,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:05,565] [INFO] Task started: CheckM
[2024-01-24 13:34:05,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/checkm_input GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:35:11,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:11,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:11,666] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:11,666] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:11,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:35:11,667] [INFO] Task started: Blastn
[2024-01-24 13:35:11,667] [INFO] Running command: blastn -query GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c8dec23-b84d-4167-8e15-98b5eca6be95/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:12,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:12,454] [INFO] Selected 32 target genomes.
[2024-01-24 13:35:12,455] [INFO] Target genome list was writen to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:12,563] [INFO] Task started: fastANI
[2024-01-24 13:35:12,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb38c8a1-fa9a-4204-bf1e-c87d81d5d481/GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna.gz --refList GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:38,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:38,414] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:38,414] [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_900112255.1	s__Flexibacter flexilis	100.0	1391	1393	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Catalimonadaceae;g__Flexibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:35:38,416] [INFO] GTDB search result was written to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:38,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:38,422] [INFO] DFAST_QC result json was written to GCF_900112255.1_IMG-taxon_2675903165_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:35:38,422] [INFO] DFAST_QC completed!
[2024-01-24 13:35:38,423] [INFO] Total running time: 0h2m28s