[2024-01-24 12:40:07,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference
[2024-01-24 12:40:09,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,313] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac2b480-661f-4d45-8654-1f33d37de3d8/GCF_007989165.1_ASM798916v1_genomic.fna.gz | prodigal -d GCF_007989165.1_ASM798916v1_genomic.fna/cds.fna -a GCF_007989165.1_ASM798916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:13,621] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:13,622] [INFO] Task started: HMMsearch
[2024-01-24 12:40:13,622] [INFO] Running command: hmmsearch --tblout GCF_007989165.1_ASM798916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/reference_markers.hmm GCF_007989165.1_ASM798916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:13,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:13,858] [INFO] Found 6/6 markers.
[2024-01-24 12:40:13,878] [INFO] Query marker FASTA was written to GCF_007989165.1_ASM798916v1_genomic.fna/markers.fasta
[2024-01-24 12:40:13,878] [INFO] Task started: Blastn
[2024-01-24 12:40:13,878] [INFO] Running command: blastn -query GCF_007989165.1_ASM798916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/reference_markers.fasta -out GCF_007989165.1_ASM798916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:14,458] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:14,462] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:14,462] [INFO] Target genome list was writen to GCF_007989165.1_ASM798916v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:14,472] [INFO] Task started: fastANI
[2024-01-24 12:40:14,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac2b480-661f-4d45-8654-1f33d37de3d8/GCF_007989165.1_ASM798916v1_genomic.fna.gz --refList GCF_007989165.1_ASM798916v1_genomic.fna/target_genomes.txt --output GCF_007989165.1_ASM798916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:18,783] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:18,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:18,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:18,792] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:40:18,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:18,792] [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=NBRC 15893	GCA_007989165.1	214326	1599	type	True	100.0	605	612	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=LT-13	GCA_002370355.1	214326	1599	type	True	99.9973	611	612	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=ATCC 15521	GCA_004354475.1	214326	1599	type	True	99.9957	610	612	95	conclusive
Latilactobacillus sakei subsp. sakei	strain=DSM 20017	GCA_001434065.1	214326	1599	type	True	99.9887	610	612	95	conclusive
Latilactobacillus sakei subsp. carnosus	strain=DSM 15831	GCA_001435715.1	214325	1599	type	True	97.1598	551	612	95	conclusive
Latilactobacillus fragifolii	strain=AMBP162	GCA_905332535.1	2814244	2814244	type	True	81.5408	322	612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:18,795] [INFO] DFAST Taxonomy check result was written to GCF_007989165.1_ASM798916v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:18,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:18,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:18,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/checkm_data
[2024-01-24 12:40:18,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:18,825] [INFO] Task started: CheckM
[2024-01-24 12:40:18,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989165.1_ASM798916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989165.1_ASM798916v1_genomic.fna/checkm_input GCF_007989165.1_ASM798916v1_genomic.fna/checkm_result
[2024-01-24 12:40:38,640] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:38,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:38,660] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:38,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:38,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989165.1_ASM798916v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:38,661] [INFO] Task started: Blastn
[2024-01-24 12:40:38,661] [INFO] Running command: blastn -query GCF_007989165.1_ASM798916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa39419d-3674-495c-bf8f-1569d1a493dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989165.1_ASM798916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:39,402] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:39,405] [INFO] Selected 8 target genomes.
[2024-01-24 12:40:39,405] [INFO] Target genome list was writen to GCF_007989165.1_ASM798916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:39,411] [INFO] Task started: fastANI
[2024-01-24 12:40:39,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac2b480-661f-4d45-8654-1f33d37de3d8/GCF_007989165.1_ASM798916v1_genomic.fna.gz --refList GCF_007989165.1_ASM798916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989165.1_ASM798916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:42,918] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:42,928] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:42,928] [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	99.9973	611	612	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	92.8974	544	612	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	82.3824	346	612	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	81.4715	322	612	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	80.1366	294	612	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 12:40:42,930] [INFO] GTDB search result was written to GCF_007989165.1_ASM798916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:42,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:42,934] [INFO] DFAST_QC result json was written to GCF_007989165.1_ASM798916v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:42,934] [INFO] DFAST_QC completed!
[2024-01-24 12:40:42,934] [INFO] Total running time: 0h0m35s