[2024-01-24 12:13:41,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:41,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:41,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference
[2024-01-24 12:13:42,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:42,957] [INFO] Task started: Prodigal
[2024-01-24 12:13:42,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg93b1864a-69d1-4b29-96fa-f28603b958ff/GCF_007989145.1_ASM798914v1_genomic.fna.gz | prodigal -d GCF_007989145.1_ASM798914v1_genomic.fna/cds.fna -a GCF_007989145.1_ASM798914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:50,410] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:50,411] [INFO] Task started: HMMsearch
[2024-01-24 12:13:50,411] [INFO] Running command: hmmsearch --tblout GCF_007989145.1_ASM798914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/reference_markers.hmm GCF_007989145.1_ASM798914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:50,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:50,768] [INFO] Found 6/6 markers.
[2024-01-24 12:13:50,797] [INFO] Query marker FASTA was written to GCF_007989145.1_ASM798914v1_genomic.fna/markers.fasta
[2024-01-24 12:13:50,798] [INFO] Task started: Blastn
[2024-01-24 12:13:50,798] [INFO] Running command: blastn -query GCF_007989145.1_ASM798914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/reference_markers.fasta -out GCF_007989145.1_ASM798914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:51,404] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:51,407] [INFO] Selected 10 target genomes.
[2024-01-24 12:13:51,407] [INFO] Target genome list was writen to GCF_007989145.1_ASM798914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:51,429] [INFO] Task started: fastANI
[2024-01-24 12:13:51,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b1864a-69d1-4b29-96fa-f28603b958ff/GCF_007989145.1_ASM798914v1_genomic.fna.gz --refList GCF_007989145.1_ASM798914v1_genomic.fna/target_genomes.txt --output GCF_007989145.1_ASM798914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:57,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:57,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:57,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:57,418] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:13:57,418] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:13:57,418] [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
Lactiplantibacillus plantarum subsp. plantarum	strain=NBRC 15891	GCA_007989145.1	337330	1590	type	True	100.0	1028	1031	95	inconclusive
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	99.9975	1030	1031	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	99.992	1023	1031	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=ATCC 14917	GCA_000143745.1	337330	1590	type	True	99.9915	1030	1031	95	inconclusive
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	95.6335	896	1031	95	inconclusive
Loigolactobacillus coryniformis subsp. coryniformis	strain=KCTC 3167	GCA_000166795.1	115541	1610	type	True	77.9862	53	1031	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.3623	66	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:57,421] [INFO] DFAST Taxonomy check result was written to GCF_007989145.1_ASM798914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:57,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:57,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:57,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/checkm_data
[2024-01-24 12:13:57,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:57,458] [INFO] Task started: CheckM
[2024-01-24 12:13:57,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989145.1_ASM798914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989145.1_ASM798914v1_genomic.fna/checkm_input GCF_007989145.1_ASM798914v1_genomic.fna/checkm_result
[2024-01-24 12:14:27,132] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:27,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,155] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:27,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:27,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989145.1_ASM798914v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:27,156] [INFO] Task started: Blastn
[2024-01-24 12:14:27,157] [INFO] Running command: blastn -query GCF_007989145.1_ASM798914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad925200-b92e-4445-abd4-22e73d5c92a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989145.1_ASM798914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:27,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:27,990] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:27,991] [INFO] Target genome list was writen to GCF_007989145.1_ASM798914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:27,998] [INFO] Task started: fastANI
[2024-01-24 12:14:27,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg93b1864a-69d1-4b29-96fa-f28603b958ff/GCF_007989145.1_ASM798914v1_genomic.fna.gz --refList GCF_007989145.1_ASM798914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989145.1_ASM798914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:35,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:35,320] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:35,320] [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_014131735.1	s__Lactiplantibacillus plantarum	99.9975	1030	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	conclusive
GCF_003641145.1	s__Lactiplantibacillus paraplantarum	87.5219	796	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	-
GCF_003641185.1	s__Lactiplantibacillus pentosus	82.6802	658	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	82.5938	643	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.39	352	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.1666	366	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.0213	361	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	79.838	319	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.5573	318	1031	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:35,326] [INFO] GTDB search result was written to GCF_007989145.1_ASM798914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:35,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:35,337] [INFO] DFAST_QC result json was written to GCF_007989145.1_ASM798914v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:35,337] [INFO] DFAST_QC completed!
[2024-01-24 12:14:35,338] [INFO] Total running time: 0h0m54s