[2024-01-25 17:37:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:05,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:05,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference
[2024-01-25 17:37:06,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:06,592] [INFO] Task started: Prodigal
[2024-01-25 17:37:06,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dcd9b2d-ea61-4cac-bedf-7b9612d3b154/GCF_003097615.1_ASM309761v1_genomic.fna.gz | prodigal -d GCF_003097615.1_ASM309761v1_genomic.fna/cds.fna -a GCF_003097615.1_ASM309761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:13,937] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:13,938] [INFO] Task started: HMMsearch
[2024-01-25 17:37:13,938] [INFO] Running command: hmmsearch --tblout GCF_003097615.1_ASM309761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/reference_markers.hmm GCF_003097615.1_ASM309761v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:14,183] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:14,184] [INFO] Found 6/6 markers.
[2024-01-25 17:37:14,213] [INFO] Query marker FASTA was written to GCF_003097615.1_ASM309761v1_genomic.fna/markers.fasta
[2024-01-25 17:37:14,213] [INFO] Task started: Blastn
[2024-01-25 17:37:14,213] [INFO] Running command: blastn -query GCF_003097615.1_ASM309761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/reference_markers.fasta -out GCF_003097615.1_ASM309761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:14,854] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:14,857] [INFO] Selected 24 target genomes.
[2024-01-25 17:37:14,857] [INFO] Target genome list was writen to GCF_003097615.1_ASM309761v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:14,863] [INFO] Task started: fastANI
[2024-01-25 17:37:14,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcd9b2d-ea61-4cac-bedf-7b9612d3b154/GCF_003097615.1_ASM309761v1_genomic.fna.gz --refList GCF_003097615.1_ASM309761v1_genomic.fna/target_genomes.txt --output GCF_003097615.1_ASM309761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:32,378] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:32,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:32,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:32,383] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:37:32,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:32,383] [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
Pueribacillus theae	strain=T8	GCA_003097615.1	2171751	2171751	type	True	100.0	1188	1195	95	conclusive
Siminovitchia thermophila	strain=DSM 105453	GCA_016909185.1	1245522	1245522	type	True	76.131	53	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:32,384] [INFO] DFAST Taxonomy check result was written to GCF_003097615.1_ASM309761v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:32,385] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:32,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:32,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/checkm_data
[2024-01-25 17:37:32,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:32,423] [INFO] Task started: CheckM
[2024-01-25 17:37:32,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003097615.1_ASM309761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003097615.1_ASM309761v1_genomic.fna/checkm_input GCF_003097615.1_ASM309761v1_genomic.fna/checkm_result
[2024-01-25 17:37:58,935] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:58,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:58,953] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:58,953] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:58,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003097615.1_ASM309761v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:58,953] [INFO] Task started: Blastn
[2024-01-25 17:37:58,954] [INFO] Running command: blastn -query GCF_003097615.1_ASM309761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45aa05d5-d943-4bca-802d-d1cd0d8bb22d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003097615.1_ASM309761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:00,052] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:00,056] [INFO] Selected 28 target genomes.
[2024-01-25 17:38:00,056] [INFO] Target genome list was writen to GCF_003097615.1_ASM309761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:00,077] [INFO] Task started: fastANI
[2024-01-25 17:38:00,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcd9b2d-ea61-4cac-bedf-7b9612d3b154/GCF_003097615.1_ASM309761v1_genomic.fna.gz --refList GCF_003097615.1_ASM309761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003097615.1_ASM309761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:20,727] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:20,731] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:20,731] [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_003097615.1	s__Pueribacillus theae	100.0	1188	1195	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Pueribacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374565.1	s__Siminovitchia fordii	77.6129	61	1195	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.95	97.34	0.95	0.89	4	-
GCA_002453275.1	s__Pueribacillus sp002453275	76.1653	80	1195	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Pueribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909185.1	s__Siminovitchia thermophila	76.131	53	1195	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.46	99.46	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:20,733] [INFO] GTDB search result was written to GCF_003097615.1_ASM309761v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:20,733] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:20,735] [INFO] DFAST_QC result json was written to GCF_003097615.1_ASM309761v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:20,735] [INFO] DFAST_QC completed!
[2024-01-25 17:38:20,735] [INFO] Total running time: 0h1m15s