[2023-06-30 04:43:29,802] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:43:29,804] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:43:29,804] [INFO] DQC Reference Directory: /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference
[2023-06-30 04:43:30,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:43:30,959] [INFO] Task started: Prodigal
[2023-06-30 04:43:30,959] [INFO] Running command: gunzip -c /var/lib/cwl/stgc92d78bb-0f85-433b-95b1-2d47a656ff2d/GCA_025367715.1_ASM2536771v1_genomic.fna.gz | prodigal -d GCA_025367715.1_ASM2536771v1_genomic.fna/cds.fna -a GCA_025367715.1_ASM2536771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:43:38,211] [INFO] Task succeeded: Prodigal
[2023-06-30 04:43:38,211] [INFO] Task started: HMMsearch
[2023-06-30 04:43:38,211] [INFO] Running command: hmmsearch --tblout GCA_025367715.1_ASM2536771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/reference_markers.hmm GCA_025367715.1_ASM2536771v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:43:38,391] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:43:38,391] [INFO] Found 6/6 markers.
[2023-06-30 04:43:38,410] [INFO] Query marker FASTA was written to GCA_025367715.1_ASM2536771v1_genomic.fna/markers.fasta
[2023-06-30 04:43:38,410] [INFO] Task started: Blastn
[2023-06-30 04:43:38,410] [INFO] Running command: blastn -query GCA_025367715.1_ASM2536771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/reference_markers.fasta -out GCA_025367715.1_ASM2536771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:43:38,975] [INFO] Task succeeded: Blastn
[2023-06-30 04:43:38,979] [INFO] Selected 37 target genomes.
[2023-06-30 04:43:38,979] [INFO] Target genome list was writen to GCA_025367715.1_ASM2536771v1_genomic.fna/target_genomes.txt
[2023-06-30 04:43:38,983] [INFO] Task started: fastANI
[2023-06-30 04:43:38,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92d78bb-0f85-433b-95b1-2d47a656ff2d/GCA_025367715.1_ASM2536771v1_genomic.fna.gz --refList GCA_025367715.1_ASM2536771v1_genomic.fna/target_genomes.txt --output GCA_025367715.1_ASM2536771v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:43:57,202] [INFO] Task succeeded: fastANI
[2023-06-30 04:43:57,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:43:57,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:43:57,206] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:43:57,206] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:43:57,207] [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
Ornithobacterium rhinotracheale	strain=DSM 15997	GCA_000265465.1	28251	28251	type	True	78.2965	61	631	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:43:57,208] [INFO] DFAST Taxonomy check result was written to GCA_025367715.1_ASM2536771v1_genomic.fna/tc_result.tsv
[2023-06-30 04:43:57,209] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:43:57,209] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:43:57,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/checkm_data
[2023-06-30 04:43:57,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:43:57,230] [INFO] Task started: CheckM
[2023-06-30 04:43:57,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025367715.1_ASM2536771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025367715.1_ASM2536771v1_genomic.fna/checkm_input GCA_025367715.1_ASM2536771v1_genomic.fna/checkm_result
[2023-06-30 04:44:23,103] [INFO] Task succeeded: CheckM
[2023-06-30 04:44:23,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:44:23,120] [INFO] ===== Completeness check finished =====
[2023-06-30 04:44:23,120] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:44:23,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025367715.1_ASM2536771v1_genomic.fna/markers.fasta)
[2023-06-30 04:44:23,121] [INFO] Task started: Blastn
[2023-06-30 04:44:23,121] [INFO] Running command: blastn -query GCA_025367715.1_ASM2536771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga112fb9a-214c-471b-9b01-2a1a15403909/dqc_reference/reference_markers_gtdb.fasta -out GCA_025367715.1_ASM2536771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:44:23,884] [INFO] Task succeeded: Blastn
[2023-06-30 04:44:23,889] [INFO] Selected 33 target genomes.
[2023-06-30 04:44:23,889] [INFO] Target genome list was writen to GCA_025367715.1_ASM2536771v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:44:23,896] [INFO] Task started: fastANI
[2023-06-30 04:44:23,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92d78bb-0f85-433b-95b1-2d47a656ff2d/GCA_025367715.1_ASM2536771v1_genomic.fna.gz --refList GCA_025367715.1_ASM2536771v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025367715.1_ASM2536771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:44:40,508] [INFO] Task succeeded: fastANI
[2023-06-30 04:44:40,513] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:44:40,513] [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_900538215.1	s__Ornithobacterium hominis	98.5561	561	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium	95.0	98.52	98.52	0.92	0.92	2	conclusive
GCF_000265465.1	s__Ornithobacterium rhinotracheale	78.2338	62	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium	95.0	99.94	99.94	0.98	0.96	3	-
GCF_009659645.1	s__Ornithobacterium rhinotracheale_B	77.1839	54	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Ornithobacterium	95.0	95.88	95.75	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-30 04:44:40,515] [INFO] GTDB search result was written to GCA_025367715.1_ASM2536771v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:44:40,516] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:44:40,518] [INFO] DFAST_QC result json was written to GCA_025367715.1_ASM2536771v1_genomic.fna/dqc_result.json
[2023-06-30 04:44:40,518] [INFO] DFAST_QC completed!
[2023-06-30 04:44:40,518] [INFO] Total running time: 0h1m11s