[2024-01-24 14:46:55,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference
[2024-01-24 14:46:58,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,022] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,022] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd112ddb-d654-473c-a274-18c276c1aef4/GCF_004354475.1_ASM435447v1_genomic.fna.gz | prodigal -d GCF_004354475.1_ASM435447v1_genomic.fna/cds.fna -a GCF_004354475.1_ASM435447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:02,267] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:02,267] [INFO] Task started: HMMsearch
[2024-01-24 14:47:02,267] [INFO] Running command: hmmsearch --tblout GCF_004354475.1_ASM435447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/reference_markers.hmm GCF_004354475.1_ASM435447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:02,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:02,499] [INFO] Found 6/6 markers.
[2024-01-24 14:47:02,519] [INFO] Query marker FASTA was written to GCF_004354475.1_ASM435447v1_genomic.fna/markers.fasta
[2024-01-24 14:47:02,519] [INFO] Task started: Blastn
[2024-01-24 14:47:02,520] [INFO] Running command: blastn -query GCF_004354475.1_ASM435447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/reference_markers.fasta -out GCF_004354475.1_ASM435447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:04,387] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:04,390] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:04,390] [INFO] Target genome list was writen to GCF_004354475.1_ASM435447v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:04,424] [INFO] Task started: fastANI
[2024-01-24 14:47:04,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd112ddb-d654-473c-a274-18c276c1aef4/GCF_004354475.1_ASM435447v1_genomic.fna.gz --refList GCF_004354475.1_ASM435447v1_genomic.fna/target_genomes.txt --output GCF_004354475.1_ASM435447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:08,963] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:08,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:08,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:08,970] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:47:08,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:08,971] [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 sakei subsp. sakei	strain=ATCC 15521	GCA_004354475.1	214326	1599	type	True	100.0	633	633	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=LT-13	GCA_002370355.1	214326	1599	type	True	99.9886	630	633	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=DSM 20017	GCA_001434065.1	214326	1599	type	True	99.9748	614	633	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=NBRC 15893	GCA_007989165.1	214326	1599	type	True	99.9509	605	633	95	conclusive
Latilactobacillus sakei subsp. carnosus	strain=DSM 15831	GCA_001435715.1	214325	1599	type	True	97.2029	561	633	95	conclusive
Latilactobacillus fragifolii	strain=AMBP162	GCA_905332535.1	2814244	2814244	type	True	81.5266	326	633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:08,972] [INFO] DFAST Taxonomy check result was written to GCF_004354475.1_ASM435447v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:08,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:08,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:08,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/checkm_data
[2024-01-24 14:47:08,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:08,997] [INFO] Task started: CheckM
[2024-01-24 14:47:08,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354475.1_ASM435447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354475.1_ASM435447v1_genomic.fna/checkm_input GCF_004354475.1_ASM435447v1_genomic.fna/checkm_result
[2024-01-24 14:47:29,969] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:29,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:29,991] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:29,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:29,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354475.1_ASM435447v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:29,992] [INFO] Task started: Blastn
[2024-01-24 14:47:29,992] [INFO] Running command: blastn -query GCF_004354475.1_ASM435447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg472f43bf-0db9-46c5-a783-6fb94d90fd6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354475.1_ASM435447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:30,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:30,802] [INFO] Selected 8 target genomes.
[2024-01-24 14:47:30,803] [INFO] Target genome list was writen to GCF_004354475.1_ASM435447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:30,839] [INFO] Task started: fastANI
[2024-01-24 14:47:30,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd112ddb-d654-473c-a274-18c276c1aef4/GCF_004354475.1_ASM435447v1_genomic.fna.gz --refList GCF_004354475.1_ASM435447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354475.1_ASM435447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:34,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:34,902] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:34,902] [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_002370355.1	s__Latilactobacillus sakei	99.9886	630	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	98.25	97.13	0.93	0.88	56	conclusive
GCF_002953655.1	s__Latilactobacillus sakei_A	92.9037	555	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004101845.1	s__Latilactobacillus curvatus	82.7158	359	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	98.79	97.67	0.89	0.82	25	-
GCF_009683145.1	s__Latilactobacillus curvatus_A	81.6345	319	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	99.02	98.50	0.90	0.86	4	-
GCF_000615805.1	s__Latilactobacillus fuchuensis	80.2635	303	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	99.39	98.80	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,904] [INFO] GTDB search result was written to GCF_004354475.1_ASM435447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:34,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:34,909] [INFO] DFAST_QC result json was written to GCF_004354475.1_ASM435447v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:34,910] [INFO] DFAST_QC completed!
[2024-01-24 14:47:34,910] [INFO] Total running time: 0h0m39s