[2024-01-24 14:14:37,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference
[2024-01-24 14:14:38,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,866] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,866] [INFO] Running command: gunzip -c /var/lib/cwl/stge5de517d-a785-4556-9fac-beb58a41b8a8/GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/cds.fna -a GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:43,990] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:43,990] [INFO] Task started: HMMsearch
[2024-01-24 14:14:43,990] [INFO] Running command: hmmsearch --tblout GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/reference_markers.hmm GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:44,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:44,284] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5de517d-a785-4556-9fac-beb58a41b8a8/GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna.gz]
[2024-01-24 14:14:44,318] [INFO] Query marker FASTA was written to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:44,318] [INFO] Task started: Blastn
[2024-01-24 14:14:44,319] [INFO] Running command: blastn -query GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/reference_markers.fasta -out GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:46,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:46,908] [INFO] Selected 23 target genomes.
[2024-01-24 14:14:46,909] [INFO] Target genome list was writen to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:46,934] [INFO] Task started: fastANI
[2024-01-24 14:14:46,934] [INFO] Running command: fastANI --query /var/lib/cwl/stge5de517d-a785-4556-9fac-beb58a41b8a8/GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna.gz --refList GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:00,114] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:00,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:00,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:00,118] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:00,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:00,119] [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
Anaerorhabdus furcosa	strain=ATCC 25662	GCA_900167375.1	118967	118967	type	True	100.0	795	795	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:15:00,120] [INFO] DFAST Taxonomy check result was written to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:00,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:00,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:00,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/checkm_data
[2024-01-24 14:15:00,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:00,154] [INFO] Task started: CheckM
[2024-01-24 14:15:00,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/checkm_input GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:22,528] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:22,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,550] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:22,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:22,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:22,551] [INFO] Task started: Blastn
[2024-01-24 14:15:22,551] [INFO] Running command: blastn -query GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c59b951-0aa1-4646-9944-296e1c21bd61/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:23,394] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:23,399] [INFO] Selected 22 target genomes.
[2024-01-24 14:15:23,399] [INFO] Target genome list was writen to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:23,466] [INFO] Task started: fastANI
[2024-01-24 14:15:23,467] [INFO] Running command: fastANI --query /var/lib/cwl/stge5de517d-a785-4556-9fac-beb58a41b8a8/GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna.gz --refList GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:31,641] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:31,673] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:31,673] [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_900167375.1	s__Anaerorhabdus furcosa	100.0	793	795	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Anaerorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012513225.1	s__UBA9076 sp012513225	76.8361	50	795	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA9076	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523895.1	s__UBA9076 sp003537975	76.7325	59	795	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA9076	95.0	98.56	98.56	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:31,675] [INFO] GTDB search result was written to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:31,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:31,678] [INFO] DFAST_QC result json was written to GCF_900167375.1_IMG-taxon_2588254259_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:15:31,679] [INFO] DFAST_QC completed!
[2024-01-24 14:15:31,679] [INFO] Total running time: 0h0m54s