[2024-01-24 11:27:20,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:20,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:20,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference
[2024-01-24 11:27:21,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:21,967] [INFO] Task started: Prodigal
[2024-01-24 11:27:21,967] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2d6f671-e95d-4e7d-88a1-04e548d1cca6/GCF_008107645.1_ASM810764v1_genomic.fna.gz | prodigal -d GCF_008107645.1_ASM810764v1_genomic.fna/cds.fna -a GCF_008107645.1_ASM810764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:25,848] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:25,849] [INFO] Task started: HMMsearch
[2024-01-24 11:27:25,849] [INFO] Running command: hmmsearch --tblout GCF_008107645.1_ASM810764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/reference_markers.hmm GCF_008107645.1_ASM810764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:26,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:26,054] [INFO] Found 6/6 markers.
[2024-01-24 11:27:26,077] [INFO] Query marker FASTA was written to GCF_008107645.1_ASM810764v1_genomic.fna/markers.fasta
[2024-01-24 11:27:26,077] [INFO] Task started: Blastn
[2024-01-24 11:27:26,077] [INFO] Running command: blastn -query GCF_008107645.1_ASM810764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/reference_markers.fasta -out GCF_008107645.1_ASM810764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:26,649] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:26,653] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:26,653] [INFO] Target genome list was writen to GCF_008107645.1_ASM810764v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:26,720] [INFO] Task started: fastANI
[2024-01-24 11:27:26,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d6f671-e95d-4e7d-88a1-04e548d1cca6/GCF_008107645.1_ASM810764v1_genomic.fna.gz --refList GCF_008107645.1_ASM810764v1_genomic.fna/target_genomes.txt --output GCF_008107645.1_ASM810764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:34,642] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:34,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:34,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:34,657] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:34,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:34,657] [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 litchii	strain=MB7	GCA_008107645.1	1981069	1981069	type	True	100.0	613	614	95	conclusive
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	82.5198	400	614	95	below_threshold
Leuconostoc mesenteroides	strain=NCTC12954	GCA_900461615.1	1245	1245	type	True	82.5077	400	614	95	below_threshold
Leuconostoc mesenteroides subsp. mesenteroides	strain=ATCC 8293	GCA_000014445.1	33967	1245	type	True	82.4801	408	614	95	below_threshold
Leuconostoc mesenteroides subsp. dextranicum	strain=DSM 20484	GCA_001047695.1	33966	1245	type	True	82.2293	390	614	95	below_threshold
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	82.2035	398	614	95	below_threshold
Leuconostoc mesenteroides subsp. cremoris	strain=ATCC 19254	GCA_000160595.1	33965	1245	type	True	82.1947	350	614	95	below_threshold
Leuconostoc mesenteroides subsp. dextranicum	strain=NBRC 100495	GCA_007990145.1	33966	1245	type	True	82.1541	377	614	95	below_threshold
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	78.9293	122	614	95	below_threshold
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	78.9135	119	614	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	78.4472	163	614	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	78.369	166	614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,659] [INFO] DFAST Taxonomy check result was written to GCF_008107645.1_ASM810764v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:34,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:34,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:34,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/checkm_data
[2024-01-24 11:27:34,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:34,680] [INFO] Task started: CheckM
[2024-01-24 11:27:34,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008107645.1_ASM810764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008107645.1_ASM810764v1_genomic.fna/checkm_input GCF_008107645.1_ASM810764v1_genomic.fna/checkm_result
[2024-01-24 11:27:53,583] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:53,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,607] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:53,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:53,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008107645.1_ASM810764v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:53,608] [INFO] Task started: Blastn
[2024-01-24 11:27:53,608] [INFO] Running command: blastn -query GCF_008107645.1_ASM810764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a0cb3f3-4090-4dbb-b853-d5297478c483/dqc_reference/reference_markers_gtdb.fasta -out GCF_008107645.1_ASM810764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:54,344] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:54,349] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:54,349] [INFO] Target genome list was writen to GCF_008107645.1_ASM810764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:54,365] [INFO] Task started: fastANI
[2024-01-24 11:27:54,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d6f671-e95d-4e7d-88a1-04e548d1cca6/GCF_008107645.1_ASM810764v1_genomic.fna.gz --refList GCF_008107645.1_ASM810764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008107645.1_ASM810764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:00,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:00,801] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:00,801] [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_008107645.1	s__Leuconostoc litchii	100.0	613	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000014445.1	s__Leuconostoc mesenteroides	82.4801	408	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	82.4259	383	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001891125.1	s__Leuconostoc suionicum	82.3266	395	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_000092505.1	s__Leuconostoc kimchii	79.8615	189	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	79.1894	197	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_012396485.1	s__Leuconostoc holzapfelii	78.9668	121	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908715.1	s__Leuconostoc rapi	78.8139	174	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165675.1	s__Leuconostoc_B fallax	78.6349	105	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc_B	95.0	99.89	99.83	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:00,804] [INFO] GTDB search result was written to GCF_008107645.1_ASM810764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:00,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:00,807] [INFO] DFAST_QC result json was written to GCF_008107645.1_ASM810764v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:00,808] [INFO] DFAST_QC completed!
[2024-01-24 11:28:00,808] [INFO] Total running time: 0h0m40s