[2024-01-24 13:57:00,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference
[2024-01-24 13:57:02,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,051] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg678996c4-cb94-45fd-930e-5cc5223a73ec/GCF_004102045.2_ASM410204v2_genomic.fna.gz | prodigal -d GCF_004102045.2_ASM410204v2_genomic.fna/cds.fna -a GCF_004102045.2_ASM410204v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:05,948] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:05,949] [INFO] Task started: HMMsearch
[2024-01-24 13:57:05,949] [INFO] Running command: hmmsearch --tblout GCF_004102045.2_ASM410204v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/reference_markers.hmm GCF_004102045.2_ASM410204v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:06,201] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:06,203] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg678996c4-cb94-45fd-930e-5cc5223a73ec/GCF_004102045.2_ASM410204v2_genomic.fna.gz]
[2024-01-24 13:57:06,225] [INFO] Query marker FASTA was written to GCF_004102045.2_ASM410204v2_genomic.fna/markers.fasta
[2024-01-24 13:57:06,225] [INFO] Task started: Blastn
[2024-01-24 13:57:06,225] [INFO] Running command: blastn -query GCF_004102045.2_ASM410204v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/reference_markers.fasta -out GCF_004102045.2_ASM410204v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,817] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:06,817] [INFO] Target genome list was writen to GCF_004102045.2_ASM410204v2_genomic.fna/target_genomes.txt
[2024-01-24 13:57:06,835] [INFO] Task started: fastANI
[2024-01-24 13:57:06,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg678996c4-cb94-45fd-930e-5cc5223a73ec/GCF_004102045.2_ASM410204v2_genomic.fna.gz --refList GCF_004102045.2_ASM410204v2_genomic.fna/target_genomes.txt --output GCF_004102045.2_ASM410204v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:11,362] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:11,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:11,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:11,368] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:11,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:11,369] [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
Oenococcus sicerae	strain=UCMA 15228	GCA_004102045.2	2203724	2203724	type	True	100.0	554	554	95	conclusive
Oenococcus oeni	strain=DSM 20252	GCA_000372485.1	1247	1247	type	True	78.1687	165	554	95	below_threshold
Oenococcus oeni	strain=DSM 20252	GCA_000309445.1	1247	1247	type	True	77.999	164	554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:11,370] [INFO] DFAST Taxonomy check result was written to GCF_004102045.2_ASM410204v2_genomic.fna/tc_result.tsv
[2024-01-24 13:57:11,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:11,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:11,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/checkm_data
[2024-01-24 13:57:11,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:11,393] [INFO] Task started: CheckM
[2024-01-24 13:57:11,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004102045.2_ASM410204v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004102045.2_ASM410204v2_genomic.fna/checkm_input GCF_004102045.2_ASM410204v2_genomic.fna/checkm_result
[2024-01-24 13:57:31,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:31,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:31,306] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:31,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:31,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004102045.2_ASM410204v2_genomic.fna/markers.fasta)
[2024-01-24 13:57:31,308] [INFO] Task started: Blastn
[2024-01-24 13:57:31,308] [INFO] Running command: blastn -query GCF_004102045.2_ASM410204v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e6adf2-d36f-4bb9-af81-ae091ba13234/dqc_reference/reference_markers_gtdb.fasta -out GCF_004102045.2_ASM410204v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:32,059] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:32,065] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:32,065] [INFO] Target genome list was writen to GCF_004102045.2_ASM410204v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:32,087] [INFO] Task started: fastANI
[2024-01-24 13:57:32,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg678996c4-cb94-45fd-930e-5cc5223a73ec/GCF_004102045.2_ASM410204v2_genomic.fna.gz --refList GCF_004102045.2_ASM410204v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004102045.2_ASM410204v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:39,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,950] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:39,950] [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_004102045.2	s__Oenococcus sicerae	100.0	553	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	98.32	98.32	0.91	0.91	2	conclusive
GCF_004010835.2	s__Oenococcus sp004010835	78.4109	173	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372485.1	s__Oenococcus oeni	78.2265	165	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	99.45	98.41	0.93	0.87	237	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,952] [INFO] GTDB search result was written to GCF_004102045.2_ASM410204v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:39,953] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:39,957] [INFO] DFAST_QC result json was written to GCF_004102045.2_ASM410204v2_genomic.fna/dqc_result.json
[2024-01-24 13:57:39,958] [INFO] DFAST_QC completed!
[2024-01-24 13:57:39,958] [INFO] Total running time: 0h0m39s