[2024-01-24 12:15:21,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:21,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:21,074] [INFO] DQC Reference Directory: /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference
[2024-01-24 12:15:22,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,463] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg3623bc67-3697-48f7-a9e5-4d03d122c7cb/GCF_024718525.1_ASM2471852v1_genomic.fna.gz | prodigal -d GCF_024718525.1_ASM2471852v1_genomic.fna/cds.fna -a GCF_024718525.1_ASM2471852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,710] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,710] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,710] [INFO] Running command: hmmsearch --tblout GCF_024718525.1_ASM2471852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/reference_markers.hmm GCF_024718525.1_ASM2471852v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:31,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:31,006] [INFO] Found 6/6 markers.
[2024-01-24 12:15:31,042] [INFO] Query marker FASTA was written to GCF_024718525.1_ASM2471852v1_genomic.fna/markers.fasta
[2024-01-24 12:15:31,043] [INFO] Task started: Blastn
[2024-01-24 12:15:31,043] [INFO] Running command: blastn -query GCF_024718525.1_ASM2471852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/reference_markers.fasta -out GCF_024718525.1_ASM2471852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,637] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,642] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:31,643] [INFO] Target genome list was writen to GCF_024718525.1_ASM2471852v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:31,650] [INFO] Task started: fastANI
[2024-01-24 12:15:31,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg3623bc67-3697-48f7-a9e5-4d03d122c7cb/GCF_024718525.1_ASM2471852v1_genomic.fna.gz --refList GCF_024718525.1_ASM2471852v1_genomic.fna/target_genomes.txt --output GCF_024718525.1_ASM2471852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:41,767] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:41,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:41,782] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:41,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:41,782] [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
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	87.8579	731	973	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	86.8318	722	973	95	below_threshold
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	83.1515	625	973	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	83.126	615	973	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	83.0948	634	973	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	82.2674	613	973	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	81.4707	449	973	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	81.4366	496	973	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	81.3408	465	973	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	80.3501	359	973	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	78.0343	90	973	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.8405	110	973	95	below_threshold
Secundilactobacillus collinoides	strain=DSM 20515	GCA_001435975.1	33960	33960	type	True	77.7817	111	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,784] [INFO] DFAST Taxonomy check result was written to GCF_024718525.1_ASM2471852v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:41,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:41,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:41,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/checkm_data
[2024-01-24 12:15:41,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:41,820] [INFO] Task started: CheckM
[2024-01-24 12:15:41,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024718525.1_ASM2471852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024718525.1_ASM2471852v1_genomic.fna/checkm_input GCF_024718525.1_ASM2471852v1_genomic.fna/checkm_result
[2024-01-24 12:16:10,709] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:10,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:10,730] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:10,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:10,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024718525.1_ASM2471852v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:10,731] [INFO] Task started: Blastn
[2024-01-24 12:16:10,731] [INFO] Running command: blastn -query GCF_024718525.1_ASM2471852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7186da9-25e3-41f3-8d8e-326942adecc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_024718525.1_ASM2471852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:11,463] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:11,468] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:11,468] [INFO] Target genome list was writen to GCF_024718525.1_ASM2471852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:11,477] [INFO] Task started: fastANI
[2024-01-24 12:16:11,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg3623bc67-3697-48f7-a9e5-4d03d122c7cb/GCF_024718525.1_ASM2471852v1_genomic.fna.gz --refList GCF_024718525.1_ASM2471852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024718525.1_ASM2471852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:20,094] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:20,111] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:20,112] [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_003666485.1	s__Levilactobacillus brevis_A	99.6054	922	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003946085.1	s__Levilactobacillus angrenensis	87.8273	733	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	86.8493	721	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861655.1	s__Levilactobacillus sp016861655	83.1366	613	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_003946045.1	s__Levilactobacillus mulengensis	83.1105	634	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861585.1	s__Levilactobacillus sp016861585	83.0283	622	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_007115095.1	s__Levilactobacillus enshiensis	81.4431	451	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861695.1	s__Levilactobacillus sp016861695	81.3859	500	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435525.1	s__Levilactobacillus koreensis	81.3408	465	973	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:20,114] [INFO] GTDB search result was written to GCF_024718525.1_ASM2471852v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:20,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:20,119] [INFO] DFAST_QC result json was written to GCF_024718525.1_ASM2471852v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:20,120] [INFO] DFAST_QC completed!
[2024-01-24 12:16:20,120] [INFO] Total running time: 0h0m59s