[2024-01-25 19:39:50,607] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference
[2024-01-25 19:39:51,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:51,748] [INFO] Task started: Prodigal
[2024-01-25 19:39:51,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7f2d42e-7c04-4cf2-a6e7-163abbf7e52b/GCF_000428085.1_ASM42808v1_genomic.fna.gz | prodigal -d GCF_000428085.1_ASM42808v1_genomic.fna/cds.fna -a GCF_000428085.1_ASM42808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:55,617] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:55,618] [INFO] Task started: HMMsearch
[2024-01-25 19:39:55,618] [INFO] Running command: hmmsearch --tblout GCF_000428085.1_ASM42808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/reference_markers.hmm GCF_000428085.1_ASM42808v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:55,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:55,797] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7f2d42e-7c04-4cf2-a6e7-163abbf7e52b/GCF_000428085.1_ASM42808v1_genomic.fna.gz]
[2024-01-25 19:39:55,816] [INFO] Query marker FASTA was written to GCF_000428085.1_ASM42808v1_genomic.fna/markers.fasta
[2024-01-25 19:39:55,816] [INFO] Task started: Blastn
[2024-01-25 19:39:55,816] [INFO] Running command: blastn -query GCF_000428085.1_ASM42808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/reference_markers.fasta -out GCF_000428085.1_ASM42808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:56,341] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:56,343] [INFO] Selected 18 target genomes.
[2024-01-25 19:39:56,344] [INFO] Target genome list was writen to GCF_000428085.1_ASM42808v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:56,356] [INFO] Task started: fastANI
[2024-01-25 19:39:56,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f2d42e-7c04-4cf2-a6e7-163abbf7e52b/GCF_000428085.1_ASM42808v1_genomic.fna.gz --refList GCF_000428085.1_ASM42808v1_genomic.fna/target_genomes.txt --output GCF_000428085.1_ASM42808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:02,806] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:02,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:02,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:02,813] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:40:02,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:02,813] [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 kitaharae	strain=DSM 17330	GCA_000428085.1	336988	336988	type	True	99.9988	610	612	95	conclusive
Oenococcus kitaharae	strain=DSM 17330	GCA_000241055.1	336988	336988	type	True	99.9945	608	612	95	conclusive
Oenococcus oeni	strain=DSM 20252	GCA_000372485.1	1247	1247	type	True	78.7262	113	612	95	below_threshold
Oenococcus oeni	strain=DSM 20252	GCA_000309445.1	1247	1247	type	True	78.409	111	612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:02,814] [INFO] DFAST Taxonomy check result was written to GCF_000428085.1_ASM42808v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:02,815] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:02,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:02,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/checkm_data
[2024-01-25 19:40:02,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:02,838] [INFO] Task started: CheckM
[2024-01-25 19:40:02,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428085.1_ASM42808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428085.1_ASM42808v1_genomic.fna/checkm_input GCF_000428085.1_ASM42808v1_genomic.fna/checkm_result
[2024-01-25 19:40:21,031] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:21,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:21,067] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:21,067] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:21,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428085.1_ASM42808v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:21,068] [INFO] Task started: Blastn
[2024-01-25 19:40:21,068] [INFO] Running command: blastn -query GCF_000428085.1_ASM42808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2591e5f0-1ef0-40ef-85a6-63ebf0a33b87/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428085.1_ASM42808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:21,839] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:21,842] [INFO] Selected 23 target genomes.
[2024-01-25 19:40:21,842] [INFO] Target genome list was writen to GCF_000428085.1_ASM42808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:21,873] [INFO] Task started: fastANI
[2024-01-25 19:40:21,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f2d42e-7c04-4cf2-a6e7-163abbf7e52b/GCF_000428085.1_ASM42808v1_genomic.fna.gz --refList GCF_000428085.1_ASM42808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428085.1_ASM42808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:30,032] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:30,035] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:30,036] [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_000241055.1	s__Oenococcus kitaharae	99.9947	607	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	99.96	99.86	0.99	0.98	5	conclusive
GCF_000372485.1	s__Oenococcus oeni	78.3951	112	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	99.45	98.41	0.93	0.87	237	-
GCF_004010835.2	s__Oenococcus sp004010835	78.3674	121	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Oenococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:30,037] [INFO] GTDB search result was written to GCF_000428085.1_ASM42808v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:30,037] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:30,039] [INFO] DFAST_QC result json was written to GCF_000428085.1_ASM42808v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:30,040] [INFO] DFAST_QC completed!
[2024-01-25 19:40:30,040] [INFO] Total running time: 0h0m39s