[2024-01-24 12:29:28,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference
[2024-01-24 12:29:29,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,508] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c1fffe7-b460-4f45-b1d5-ddf054397337/GCF_000732905.1_ASM73290v1_genomic.fna.gz | prodigal -d GCF_000732905.1_ASM73290v1_genomic.fna/cds.fna -a GCF_000732905.1_ASM73290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:33,143] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:33,143] [INFO] Task started: HMMsearch
[2024-01-24 12:29:33,143] [INFO] Running command: hmmsearch --tblout GCF_000732905.1_ASM73290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/reference_markers.hmm GCF_000732905.1_ASM73290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:33,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:33,439] [INFO] Found 6/6 markers.
[2024-01-24 12:29:33,455] [INFO] Query marker FASTA was written to GCF_000732905.1_ASM73290v1_genomic.fna/markers.fasta
[2024-01-24 12:29:33,456] [INFO] Task started: Blastn
[2024-01-24 12:29:33,456] [INFO] Running command: blastn -query GCF_000732905.1_ASM73290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/reference_markers.fasta -out GCF_000732905.1_ASM73290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:34,070] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:34,073] [INFO] Selected 18 target genomes.
[2024-01-24 12:29:34,073] [INFO] Target genome list was writen to GCF_000732905.1_ASM73290v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:34,116] [INFO] Task started: fastANI
[2024-01-24 12:29:34,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c1fffe7-b460-4f45-b1d5-ddf054397337/GCF_000732905.1_ASM73290v1_genomic.fna.gz --refList GCF_000732905.1_ASM73290v1_genomic.fna/target_genomes.txt --output GCF_000732905.1_ASM73290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:40,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:40,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:40,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:40,451] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:40,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:40,452] [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 ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	83.9877	323	451	95	below_threshold
Weissella jogaejeotgali	strain=FOL01	GCA_001932615.1	1631871	1631871	type	True	80.3852	75	451	95	below_threshold
Weissella coleopterorum	strain=HDW19	GCA_011304355.1	2714949	2714949	type	True	79.9876	57	451	95	below_threshold
Weissella viridescens	strain=NCTC13645	GCA_900460455.1	1629	1629	type	True	79.9452	108	451	95	below_threshold
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	79.5629	94	451	95	below_threshold
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	79.3845	109	451	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	79.1117	117	451	95	below_threshold
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	79.0777	113	451	95	below_threshold
Weissella minor	strain=DSM 20014	GCA_001437425.1	1620	1620	type	True	79.0098	134	451	95	below_threshold
Weissella uvarum	strain=DSM 28060	GCA_016908785.1	1479233	1479233	type	True	78.8172	106	451	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	78.7602	102	451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:40,454] [INFO] DFAST Taxonomy check result was written to GCF_000732905.1_ASM73290v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:40,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:40,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:40,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/checkm_data
[2024-01-24 12:29:40,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:40,486] [INFO] Task started: CheckM
[2024-01-24 12:29:40,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000732905.1_ASM73290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000732905.1_ASM73290v1_genomic.fna/checkm_input GCF_000732905.1_ASM73290v1_genomic.fna/checkm_result
[2024-01-24 12:29:59,200] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:59,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:59,222] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:59,222] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:59,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000732905.1_ASM73290v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:59,223] [INFO] Task started: Blastn
[2024-01-24 12:29:59,223] [INFO] Running command: blastn -query GCF_000732905.1_ASM73290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg599411ce-d941-471c-81af-a0b1e953325a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000732905.1_ASM73290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:59,968] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:59,972] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:59,972] [INFO] Target genome list was writen to GCF_000732905.1_ASM73290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:59,982] [INFO] Task started: fastANI
[2024-01-24 12:29:59,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c1fffe7-b460-4f45-b1d5-ddf054397337/GCF_000732905.1_ASM73290v1_genomic.fna.gz --refList GCF_000732905.1_ASM73290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000732905.1_ASM73290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:05,016] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:05,026] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:05,027] [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_000750535.1	s__Weissella ceti_A	99.9553	447	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.87	99.79	0.99	0.98	5	conclusive
GCF_018394055.1	s__Weissella ceti	84.0159	323	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011304355.1	s__Weissella coleopterorum	79.8866	57	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004766315.1	s__Weissella confusa_A	79.5599	121	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003862435.1	s__Weissella viridescens_A	79.5073	115	451	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	79.3178	126	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_008107635.1	s__Weissella muntiaci	79.2435	61	451	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	79.0877	111	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_001437425.1	s__Weissella minor	79.0098	134	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
GCF_004521965.1	s__Weissella cibaria_A	78.9905	99	451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908785.1	s__Weissella uvarum	78.8172	106	451	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 12:30:05,028] [INFO] GTDB search result was written to GCF_000732905.1_ASM73290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:05,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:05,039] [INFO] DFAST_QC result json was written to GCF_000732905.1_ASM73290v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:05,040] [INFO] DFAST_QC completed!
[2024-01-24 12:30:05,040] [INFO] Total running time: 0h0m37s