[2024-01-24 12:31:51,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference
[2024-01-24 12:31:52,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,787] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,787] [INFO] Running command: gunzip -c /var/lib/cwl/stga988eb83-713c-4d07-b4bb-c9a0946ac391/GCF_001434175.1_ASM143417v1_genomic.fna.gz | prodigal -d GCF_001434175.1_ASM143417v1_genomic.fna/cds.fna -a GCF_001434175.1_ASM143417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:00,039] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:00,040] [INFO] Task started: HMMsearch
[2024-01-24 12:32:00,040] [INFO] Running command: hmmsearch --tblout GCF_001434175.1_ASM143417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/reference_markers.hmm GCF_001434175.1_ASM143417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:00,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:00,300] [INFO] Found 6/6 markers.
[2024-01-24 12:32:00,334] [INFO] Query marker FASTA was written to GCF_001434175.1_ASM143417v1_genomic.fna/markers.fasta
[2024-01-24 12:32:00,335] [INFO] Task started: Blastn
[2024-01-24 12:32:00,335] [INFO] Running command: blastn -query GCF_001434175.1_ASM143417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/reference_markers.fasta -out GCF_001434175.1_ASM143417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:00,936] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:00,941] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:00,941] [INFO] Target genome list was writen to GCF_001434175.1_ASM143417v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:00,950] [INFO] Task started: fastANI
[2024-01-24 12:32:00,950] [INFO] Running command: fastANI --query /var/lib/cwl/stga988eb83-713c-4d07-b4bb-c9a0946ac391/GCF_001434175.1_ASM143417v1_genomic.fna.gz --refList GCF_001434175.1_ASM143417v1_genomic.fna/target_genomes.txt --output GCF_001434175.1_ASM143417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:07,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:07,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:07,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:07,084] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:32:07,084] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:32:07,084] [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=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	100.0	1048	1048	95	inconclusive
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	99.9884	1048	1048	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=ATCC 14917	GCA_000143745.1	337330	1590	type	True	99.9826	1045	1048	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=NBRC 15891	GCA_007989145.1	337330	1590	type	True	99.9736	1019	1048	95	inconclusive
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	95.6352	913	1048	95	inconclusive
Loigolactobacillus coryniformis subsp. coryniformis	strain=KCTC 3167	GCA_000166795.1	115541	1610	type	True	78.0212	56	1048	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.4765	66	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,086] [INFO] DFAST Taxonomy check result was written to GCF_001434175.1_ASM143417v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:07,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:07,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:07,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/checkm_data
[2024-01-24 12:32:07,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:07,129] [INFO] Task started: CheckM
[2024-01-24 12:32:07,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434175.1_ASM143417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434175.1_ASM143417v1_genomic.fna/checkm_input GCF_001434175.1_ASM143417v1_genomic.fna/checkm_result
[2024-01-24 12:32:35,096] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:35,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,122] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:35,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:35,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434175.1_ASM143417v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:35,124] [INFO] Task started: Blastn
[2024-01-24 12:32:35,124] [INFO] Running command: blastn -query GCF_001434175.1_ASM143417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46209f1e-5bd9-45ed-bece-f76dd3893d36/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434175.1_ASM143417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:35,894] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:35,898] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:35,898] [INFO] Target genome list was writen to GCF_001434175.1_ASM143417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:35,912] [INFO] Task started: fastANI
[2024-01-24 12:32:35,912] [INFO] Running command: fastANI --query /var/lib/cwl/stga988eb83-713c-4d07-b4bb-c9a0946ac391/GCF_001434175.1_ASM143417v1_genomic.fna.gz --refList GCF_001434175.1_ASM143417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434175.1_ASM143417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:43,149] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:43,165] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:43,166] [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	99.9884	1048	1048	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	87.7118	812	1048	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	82.634	661	1048	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	82.6339	647	1048	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.4897	355	1048	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	80.3128	348	1048	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.2244	370	1048	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	79.8703	331	1048	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	79.6924	325	1048	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 12:32:43,167] [INFO] GTDB search result was written to GCF_001434175.1_ASM143417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:43,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:43,171] [INFO] DFAST_QC result json was written to GCF_001434175.1_ASM143417v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:43,171] [INFO] DFAST_QC completed!
[2024-01-24 12:32:43,172] [INFO] Total running time: 0h0m52s