[2024-01-24 14:19:31,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference
[2024-01-24 14:19:32,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:32,575] [INFO] Task started: Prodigal
[2024-01-24 14:19:32,575] [INFO] Running command: gunzip -c /var/lib/cwl/stgee1cb1d5-85fa-4f74-a91d-bbaa5df735f6/GCF_006540285.1_ASM654028v1_genomic.fna.gz | prodigal -d GCF_006540285.1_ASM654028v1_genomic.fna/cds.fna -a GCF_006540285.1_ASM654028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:36,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:36,883] [INFO] Task started: HMMsearch
[2024-01-24 14:19:36,884] [INFO] Running command: hmmsearch --tblout GCF_006540285.1_ASM654028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/reference_markers.hmm GCF_006540285.1_ASM654028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:37,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:37,144] [INFO] Found 6/6 markers.
[2024-01-24 14:19:37,165] [INFO] Query marker FASTA was written to GCF_006540285.1_ASM654028v1_genomic.fna/markers.fasta
[2024-01-24 14:19:37,165] [INFO] Task started: Blastn
[2024-01-24 14:19:37,165] [INFO] Running command: blastn -query GCF_006540285.1_ASM654028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/reference_markers.fasta -out GCF_006540285.1_ASM654028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:37,766] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:37,769] [INFO] Selected 9 target genomes.
[2024-01-24 14:19:37,770] [INFO] Target genome list was writen to GCF_006540285.1_ASM654028v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:37,793] [INFO] Task started: fastANI
[2024-01-24 14:19:37,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1cb1d5-85fa-4f74-a91d-bbaa5df735f6/GCF_006540285.1_ASM654028v1_genomic.fna.gz --refList GCF_006540285.1_ASM654028v1_genomic.fna/target_genomes.txt --output GCF_006540285.1_ASM654028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:41,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:41,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:41,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:41,865] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:41,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:41,865] [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
Latilactobacillus curvatus	strain=NBRC 15884	GCA_006540285.1	28038	28038	type	True	100.0	563	565	95	conclusive
Latilactobacillus curvatus	strain=DSM 20019	GCA_004101845.1	28038	28038	type	True	99.9993	565	565	95	conclusive
Latilactobacillus curvatus	strain=DSM 20019	GCA_001435495.1	28038	28038	type	True	99.7994	479	565	95	conclusive
Latilactobacillus fragifolii	strain=AMBP162	GCA_905332535.1	2814244	2814244	type	True	88.4816	456	565	95	below_threshold
Latilactobacillus graminis	strain=DSM 20719	GCA_001436415.1	60519	60519	type	True	84.6731	397	565	95	below_threshold
Latilactobacillus sakei subsp. carnosus	strain=DSM 15831	GCA_001435715.1	214325	1599	type	True	82.7373	331	565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:41,873] [INFO] DFAST Taxonomy check result was written to GCF_006540285.1_ASM654028v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:41,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:41,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:41,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/checkm_data
[2024-01-24 14:19:41,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:41,907] [INFO] Task started: CheckM
[2024-01-24 14:19:41,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540285.1_ASM654028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540285.1_ASM654028v1_genomic.fna/checkm_input GCF_006540285.1_ASM654028v1_genomic.fna/checkm_result
[2024-01-24 14:20:03,143] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:03,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:03,164] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:03,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:03,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540285.1_ASM654028v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:03,166] [INFO] Task started: Blastn
[2024-01-24 14:20:03,166] [INFO] Running command: blastn -query GCF_006540285.1_ASM654028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb44c3896-3600-4ba5-84be-8a682e8c75e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540285.1_ASM654028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,977] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:03,977] [INFO] Target genome list was writen to GCF_006540285.1_ASM654028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:03,983] [INFO] Task started: fastANI
[2024-01-24 14:20:03,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgee1cb1d5-85fa-4f74-a91d-bbaa5df735f6/GCF_006540285.1_ASM654028v1_genomic.fna.gz --refList GCF_006540285.1_ASM654028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540285.1_ASM654028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:07,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:07,128] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:07,128] [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_004101845.1	s__Latilactobacillus curvatus	99.9993	565	565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	98.79	97.67	0.89	0.82	25	conclusive
GCF_009683145.1	s__Latilactobacillus curvatus_A	88.5282	447	565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	99.02	98.50	0.90	0.86	4	-
GCF_001436415.1	s__Latilactobacillus graminis	84.6751	396	565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002370355.1	s__Latilactobacillus sakei	82.7272	330	565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	98.25	97.13	0.93	0.88	56	-
GCF_002953655.1	s__Latilactobacillus sakei_A	82.4375	329	565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:07,130] [INFO] GTDB search result was written to GCF_006540285.1_ASM654028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:07,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:07,133] [INFO] DFAST_QC result json was written to GCF_006540285.1_ASM654028v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:07,133] [INFO] DFAST_QC completed!
[2024-01-24 14:20:07,133] [INFO] Total running time: 0h0m36s