[2024-01-24 15:32:05,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference
[2024-01-24 15:32:06,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,712] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2f83c91-be32-4651-83ce-2e821029dd07/GCF_007991555.1_ASM799155v1_genomic.fna.gz | prodigal -d GCF_007991555.1_ASM799155v1_genomic.fna/cds.fna -a GCF_007991555.1_ASM799155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:11,112] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:11,113] [INFO] Task started: HMMsearch
[2024-01-24 15:32:11,113] [INFO] Running command: hmmsearch --tblout GCF_007991555.1_ASM799155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/reference_markers.hmm GCF_007991555.1_ASM799155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:11,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:11,346] [INFO] Found 6/6 markers.
[2024-01-24 15:32:11,370] [INFO] Query marker FASTA was written to GCF_007991555.1_ASM799155v1_genomic.fna/markers.fasta
[2024-01-24 15:32:11,371] [INFO] Task started: Blastn
[2024-01-24 15:32:11,371] [INFO] Running command: blastn -query GCF_007991555.1_ASM799155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/reference_markers.fasta -out GCF_007991555.1_ASM799155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:11,956] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:11,960] [INFO] Selected 17 target genomes.
[2024-01-24 15:32:11,960] [INFO] Target genome list was writen to GCF_007991555.1_ASM799155v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:11,968] [INFO] Task started: fastANI
[2024-01-24 15:32:11,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f83c91-be32-4651-83ce-2e821029dd07/GCF_007991555.1_ASM799155v1_genomic.fna.gz --refList GCF_007991555.1_ASM799155v1_genomic.fna/target_genomes.txt --output GCF_007991555.1_ASM799155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:17,420] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:17,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:17,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:17,429] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:32:17,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:17,429] [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 soli	strain=KACC 11848	GCA_001761545.1	155866	155866	type	True	99.9991	545	546	95	conclusive
Weissella soli	strain=CCUG 46608	GCA_012396465.1	155866	155866	type	True	99.9989	545	546	95	conclusive
Weissella koreensis	strain=KCTC 3621	GCA_000277645.1	165096	165096	type	True	78.7346	57	546	95	below_threshold
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	78.4534	95	546	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	78.4158	93	546	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	78.3673	64	546	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	78.2853	64	546	95	below_threshold
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	78.1895	65	546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:17,431] [INFO] DFAST Taxonomy check result was written to GCF_007991555.1_ASM799155v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:17,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:17,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:17,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/checkm_data
[2024-01-24 15:32:17,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:17,461] [INFO] Task started: CheckM
[2024-01-24 15:32:17,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991555.1_ASM799155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991555.1_ASM799155v1_genomic.fna/checkm_input GCF_007991555.1_ASM799155v1_genomic.fna/checkm_result
[2024-01-24 15:32:37,615] [INFO] Task succeeded: CheckM
[2024-01-24 15:32:37,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:32:37,637] [INFO] ===== Completeness check finished =====
[2024-01-24 15:32:37,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:32:37,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991555.1_ASM799155v1_genomic.fna/markers.fasta)
[2024-01-24 15:32:37,638] [INFO] Task started: Blastn
[2024-01-24 15:32:37,638] [INFO] Running command: blastn -query GCF_007991555.1_ASM799155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ffe803-d29c-41a7-bce2-19f4a80cff32/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991555.1_ASM799155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:38,409] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:38,413] [INFO] Selected 22 target genomes.
[2024-01-24 15:32:38,413] [INFO] Target genome list was writen to GCF_007991555.1_ASM799155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:32:38,446] [INFO] Task started: fastANI
[2024-01-24 15:32:38,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f83c91-be32-4651-83ce-2e821029dd07/GCF_007991555.1_ASM799155v1_genomic.fna.gz --refList GCF_007991555.1_ASM799155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991555.1_ASM799155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:32:45,789] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:45,804] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:32:45,805] [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_001761545.1	s__Weissella soli	99.9991	545	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.70	98.78	0.98	0.93	5	conclusive
GCA_001436895.1	s__Weissella confusa	78.8283	107	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_004521965.1	s__Weissella cibaria_A	78.777	89	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004771295.1	s__Weissella confusa_B	78.7485	106	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCF_000277645.1	s__Weissella koreensis	78.6589	59	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_004766315.1	s__Weissella confusa_A	78.5494	104	546	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	78.48	94	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_005405465.1	s__Weissella thailandensis	78.4598	62	546	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_018394055.1	s__Weissella ceti	78.2485	64	546	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	78.2018	66	546	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 15:32:45,806] [INFO] GTDB search result was written to GCF_007991555.1_ASM799155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:32:45,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:32:45,810] [INFO] DFAST_QC result json was written to GCF_007991555.1_ASM799155v1_genomic.fna/dqc_result.json
[2024-01-24 15:32:45,810] [INFO] DFAST_QC completed!
[2024-01-24 15:32:45,810] [INFO] Total running time: 0h0m40s