[2024-01-24 11:20:18,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:18,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:18,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference
[2024-01-24 11:20:20,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,221] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg081819cc-545d-4a08-a032-3b24bbf51abe/GCF_008107635.1_ASM810763v1_genomic.fna.gz | prodigal -d GCF_008107635.1_ASM810763v1_genomic.fna/cds.fna -a GCF_008107635.1_ASM810763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:25,424] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:25,424] [INFO] Task started: HMMsearch
[2024-01-24 11:20:25,425] [INFO] Running command: hmmsearch --tblout GCF_008107635.1_ASM810763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/reference_markers.hmm GCF_008107635.1_ASM810763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:25,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:25,669] [INFO] Found 6/6 markers.
[2024-01-24 11:20:25,691] [INFO] Query marker FASTA was written to GCF_008107635.1_ASM810763v1_genomic.fna/markers.fasta
[2024-01-24 11:20:25,692] [INFO] Task started: Blastn
[2024-01-24 11:20:25,692] [INFO] Running command: blastn -query GCF_008107635.1_ASM810763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/reference_markers.fasta -out GCF_008107635.1_ASM810763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:26,291] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:26,294] [INFO] Selected 25 target genomes.
[2024-01-24 11:20:26,294] [INFO] Target genome list was writen to GCF_008107635.1_ASM810763v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:26,422] [INFO] Task started: fastANI
[2024-01-24 11:20:26,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg081819cc-545d-4a08-a032-3b24bbf51abe/GCF_008107635.1_ASM810763v1_genomic.fna.gz --refList GCF_008107635.1_ASM810763v1_genomic.fna/target_genomes.txt --output GCF_008107635.1_ASM810763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:34,298] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:34,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:34,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:34,315] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:34,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:34,316] [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
Weissella muntiaci	strain=8H-2	GCA_008107635.1	2508881	2508881	type	True	100.0	741	744	95	conclusive
Weissella oryzae	strain=SG25	GCA_000691805.2	1129792	1129792	type	True	80.1132	228	744	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	79.1663	80	744	95	below_threshold
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	79.044	79	744	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	78.758	65	744	95	below_threshold
Weissella hellenica	strain=CCUG 33494	GCA_012396435.1	46256	46256	suspected-type	True	78.7208	73	744	95	below_threshold
Weissella uvarum	strain=DSM 28060	GCA_016908785.1	1479233	1479233	type	True	78.681	64	744	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_005405545.1	46256	46256	suspected-type	True	78.5636	72	744	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	78.4772	71	744	95	below_threshold
Weissella minor	strain=DSM 20014	GCA_001437425.1	1620	1620	type	True	78.2991	74	744	95	below_threshold
Weissella thailandensis	strain=JCM 10695	GCA_005405465.1	89061	89061	type	True	78.2878	80	744	95	below_threshold
Weissella thailandensis	strain=KCTC 3751	GCA_003363255.1	89061	89061	type	True	78.2032	80	744	95	below_threshold
Weissella thailandensis	strain=CCUG 46557	GCA_012396385.1	89061	89061	type	True	77.9721	79	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:34,317] [INFO] DFAST Taxonomy check result was written to GCF_008107635.1_ASM810763v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:34,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:34,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:34,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/checkm_data
[2024-01-24 11:20:34,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:34,353] [INFO] Task started: CheckM
[2024-01-24 11:20:34,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008107635.1_ASM810763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008107635.1_ASM810763v1_genomic.fna/checkm_input GCF_008107635.1_ASM810763v1_genomic.fna/checkm_result
[2024-01-24 11:20:57,256] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:57,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:57,280] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:57,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:57,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008107635.1_ASM810763v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:57,281] [INFO] Task started: Blastn
[2024-01-24 11:20:57,281] [INFO] Running command: blastn -query GCF_008107635.1_ASM810763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7518e70c-eef5-483d-9759-db807448a915/dqc_reference/reference_markers_gtdb.fasta -out GCF_008107635.1_ASM810763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:58,028] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:58,032] [INFO] Selected 22 target genomes.
[2024-01-24 11:20:58,033] [INFO] Target genome list was writen to GCF_008107635.1_ASM810763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:58,052] [INFO] Task started: fastANI
[2024-01-24 11:20:58,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg081819cc-545d-4a08-a032-3b24bbf51abe/GCF_008107635.1_ASM810763v1_genomic.fna.gz --refList GCF_008107635.1_ASM810763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008107635.1_ASM810763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:05,056] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:05,071] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:05,071] [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_008107635.1	s__Weissella muntiaci	100.0	741	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000691805.2	s__Weissella oryzae	80.1014	228	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001436895.1	s__Weissella confusa	79.5064	82	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_004766315.1	s__Weissella confusa_A	79.0754	74	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521965.1	s__Weissella cibaria_A	79.058	73	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193635.1	s__Weissella cibaria	79.044	79	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_000750535.1	s__Weissella ceti_A	78.9614	58	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.87	99.79	0.99	0.98	5	-
GCF_004771295.1	s__Weissella confusa_B	78.7865	84	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCF_016908785.1	s__Weissella uvarum	78.6511	65	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405545.1	s__Weissella hellenica	78.5071	73	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	99.99	0.99	0.99	4	-
GCF_005405465.1	s__Weissella thailandensis	78.2878	80	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_001437425.1	s__Weissella minor	78.2821	75	744	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,073] [INFO] GTDB search result was written to GCF_008107635.1_ASM810763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:05,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:05,077] [INFO] DFAST_QC result json was written to GCF_008107635.1_ASM810763v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:05,077] [INFO] DFAST_QC completed!
[2024-01-24 11:21:05,077] [INFO] Total running time: 0h0m46s