[2024-01-24 11:34:39,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,580] [INFO] DQC Reference Directory: /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference
[2024-01-24 11:34:40,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:40,854] [INFO] Task started: Prodigal
[2024-01-24 11:34:40,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg7810cba9-d693-4f23-8072-efd6ec389225/GCF_023657405.1_ASM2365740v1_genomic.fna.gz | prodigal -d GCF_023657405.1_ASM2365740v1_genomic.fna/cds.fna -a GCF_023657405.1_ASM2365740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:44,878] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:44,879] [INFO] Task started: HMMsearch
[2024-01-24 11:34:44,879] [INFO] Running command: hmmsearch --tblout GCF_023657405.1_ASM2365740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/reference_markers.hmm GCF_023657405.1_ASM2365740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:45,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:45,250] [INFO] Found 6/6 markers.
[2024-01-24 11:34:45,279] [INFO] Query marker FASTA was written to GCF_023657405.1_ASM2365740v1_genomic.fna/markers.fasta
[2024-01-24 11:34:45,280] [INFO] Task started: Blastn
[2024-01-24 11:34:45,280] [INFO] Running command: blastn -query GCF_023657405.1_ASM2365740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/reference_markers.fasta -out GCF_023657405.1_ASM2365740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:46,476] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:46,479] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:46,480] [INFO] Target genome list was writen to GCF_023657405.1_ASM2365740v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:46,494] [INFO] Task started: fastANI
[2024-01-24 11:34:46,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg7810cba9-d693-4f23-8072-efd6ec389225/GCF_023657405.1_ASM2365740v1_genomic.fna.gz --refList GCF_023657405.1_ASM2365740v1_genomic.fna/target_genomes.txt --output GCF_023657405.1_ASM2365740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:50,710] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:50,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:50,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:50,721] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:34:50,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:50,722] [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 uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	100.0	553	553	95	conclusive
Weissella uvarum	strain=DSM 28060	GCA_016908785.1	1479233	1479233	type	True	99.9956	551	553	95	conclusive
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	80.2016	166	553	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	80.0518	188	553	95	below_threshold
Weissella minor	strain=DSM 20014	GCA_001437425.1	1620	1620	type	True	79.9089	222	553	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	78.3155	102	553	95	below_threshold
Weissella bombi	strain=DSM 28794	GCA_005405505.1	1505725	1505725	type	True	78.2881	101	553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:50,725] [INFO] DFAST Taxonomy check result was written to GCF_023657405.1_ASM2365740v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:50,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:50,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:50,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/checkm_data
[2024-01-24 11:34:50,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:50,750] [INFO] Task started: CheckM
[2024-01-24 11:34:50,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023657405.1_ASM2365740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023657405.1_ASM2365740v1_genomic.fna/checkm_input GCF_023657405.1_ASM2365740v1_genomic.fna/checkm_result
[2024-01-24 11:35:10,993] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:10,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:11,025] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:11,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:11,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023657405.1_ASM2365740v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:11,026] [INFO] Task started: Blastn
[2024-01-24 11:35:11,026] [INFO] Running command: blastn -query GCF_023657405.1_ASM2365740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf60f0b05-9ad7-4091-8962-32153820b1cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_023657405.1_ASM2365740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:11,878] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:11,882] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:11,882] [INFO] Target genome list was writen to GCF_023657405.1_ASM2365740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:11,892] [INFO] Task started: fastANI
[2024-01-24 11:35:11,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg7810cba9-d693-4f23-8072-efd6ec389225/GCF_023657405.1_ASM2365740v1_genomic.fna.gz --refList GCF_023657405.1_ASM2365740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023657405.1_ASM2365740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:16,513] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:16,522] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:16,523] [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_016908785.1	s__Weissella uvarum	99.9956	551	553	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_001437355.1	s__Weissella viridescens	80.0232	189	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.44	98.29	0.96	0.91	6	-
GCF_001437425.1	s__Weissella minor	79.9089	222	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
GCF_003862435.1	s__Weissella viridescens_A	79.7638	212	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018394055.1	s__Weissella ceti	78.9709	105	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000277645.1	s__Weissella koreensis	78.6912	53	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_000160575.1	s__Weissella paramesenteroides	78.6107	90	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.27	97.99	0.88	0.85	25	-
GCF_001438705.1	s__Weissella kandleri	78.5655	54	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094835.1	s__Weissella bombi	78.3301	101	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004521965.1	s__Weissella cibaria_A	78.2241	91	553	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:16,524] [INFO] GTDB search result was written to GCF_023657405.1_ASM2365740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:16,525] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:16,528] [INFO] DFAST_QC result json was written to GCF_023657405.1_ASM2365740v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:16,528] [INFO] DFAST_QC completed!
[2024-01-24 11:35:16,528] [INFO] Total running time: 0h0m37s