[2024-01-24 13:49:17,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:17,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:17,540] [INFO] DQC Reference Directory: /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference
[2024-01-24 13:49:18,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:18,867] [INFO] Task started: Prodigal
[2024-01-24 13:49:18,868] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8b7aaf0-d717-4018-989e-1b2df8827f60/GCF_007990165.1_ASM799016v1_genomic.fna.gz | prodigal -d GCF_007990165.1_ASM799016v1_genomic.fna/cds.fna -a GCF_007990165.1_ASM799016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,514] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,515] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,515] [INFO] Running command: hmmsearch --tblout GCF_007990165.1_ASM799016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/reference_markers.hmm GCF_007990165.1_ASM799016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:23,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:23,749] [INFO] Found 6/6 markers.
[2024-01-24 13:49:23,770] [INFO] Query marker FASTA was written to GCF_007990165.1_ASM799016v1_genomic.fna/markers.fasta
[2024-01-24 13:49:23,771] [INFO] Task started: Blastn
[2024-01-24 13:49:23,771] [INFO] Running command: blastn -query GCF_007990165.1_ASM799016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/reference_markers.fasta -out GCF_007990165.1_ASM799016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,367] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,369] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:24,370] [INFO] Target genome list was writen to GCF_007990165.1_ASM799016v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,374] [INFO] Task started: fastANI
[2024-01-24 13:49:24,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b7aaf0-d717-4018-989e-1b2df8827f60/GCF_007990165.1_ASM799016v1_genomic.fna.gz --refList GCF_007990165.1_ASM799016v1_genomic.fna/target_genomes.txt --output GCF_007990165.1_ASM799016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:28,642] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:28,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:28,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:28,650] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:49:28,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:28,651] [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
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	100.0	662	662	95	conclusive
Leuconostoc mesenteroides subsp. mesenteroides	strain=ATCC 8293	GCA_000014445.1	33967	1245	type	True	99.9985	661	662	95	conclusive
Leuconostoc mesenteroides	strain=NCTC12954	GCA_900461615.1	1245	1245	type	True	99.9963	661	662	95	conclusive
Leuconostoc mesenteroides subsp. dextranicum	strain=NBRC 100495	GCA_007990145.1	33966	1245	type	True	98.9073	513	662	95	conclusive
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	98.7823	592	662	95	conclusive
Leuconostoc mesenteroides subsp. cremoris	strain=ATCC 19254	GCA_000160595.1	33965	1245	type	True	98.2752	477	662	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,652] [INFO] DFAST Taxonomy check result was written to GCF_007990165.1_ASM799016v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:28,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:28,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:28,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/checkm_data
[2024-01-24 13:49:28,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:28,681] [INFO] Task started: CheckM
[2024-01-24 13:49:28,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990165.1_ASM799016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990165.1_ASM799016v1_genomic.fna/checkm_input GCF_007990165.1_ASM799016v1_genomic.fna/checkm_result
[2024-01-24 13:49:50,780] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:50,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,799] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:50,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:50,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990165.1_ASM799016v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:50,800] [INFO] Task started: Blastn
[2024-01-24 13:49:50,800] [INFO] Running command: blastn -query GCF_007990165.1_ASM799016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga693215d-6e4b-4d53-b04a-eea67d02f52d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990165.1_ASM799016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,575] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:51,575] [INFO] Target genome list was writen to GCF_007990165.1_ASM799016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,585] [INFO] Task started: fastANI
[2024-01-24 13:49:51,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b7aaf0-d717-4018-989e-1b2df8827f60/GCF_007990165.1_ASM799016v1_genomic.fna.gz --refList GCF_007990165.1_ASM799016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990165.1_ASM799016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:56,289] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:56,298] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:56,299] [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_000014445.1	s__Leuconostoc mesenteroides	99.9985	661	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	conclusive
GCF_001891125.1	s__Leuconostoc suionicum	94.2183	580	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	91.0727	513	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008107645.1	s__Leuconostoc litchii	82.3472	417	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092505.1	s__Leuconostoc kimchii	81.0109	184	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_014634805.1	s__Leuconostoc falkenbergense	80.6188	212	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	-
GCF_007954625.1	s__Leuconostoc lactis_A	80.4619	135	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	80.0204	221	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_016908715.1	s__Leuconostoc rapi	79.9072	176	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207505.1	s__Leuconostoc carnosum	79.326	177	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,300] [INFO] GTDB search result was written to GCF_007990165.1_ASM799016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:56,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:56,305] [INFO] DFAST_QC result json was written to GCF_007990165.1_ASM799016v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:56,305] [INFO] DFAST_QC completed!
[2024-01-24 13:49:56,305] [INFO] Total running time: 0h0m39s