[2024-01-25 20:18:35,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:35,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:35,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference
[2024-01-25 20:18:36,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:36,696] [INFO] Task started: Prodigal
[2024-01-25 20:18:36,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbd01c49-4c28-4d2d-b4dd-eb9030a206da/GCF_003946045.1_ASM394604v1_genomic.fna.gz | prodigal -d GCF_003946045.1_ASM394604v1_genomic.fna/cds.fna -a GCF_003946045.1_ASM394604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:43,653] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:43,654] [INFO] Task started: HMMsearch
[2024-01-25 20:18:43,654] [INFO] Running command: hmmsearch --tblout GCF_003946045.1_ASM394604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/reference_markers.hmm GCF_003946045.1_ASM394604v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:43,863] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:43,864] [INFO] Found 6/6 markers.
[2024-01-25 20:18:43,892] [INFO] Query marker FASTA was written to GCF_003946045.1_ASM394604v1_genomic.fna/markers.fasta
[2024-01-25 20:18:43,892] [INFO] Task started: Blastn
[2024-01-25 20:18:43,892] [INFO] Running command: blastn -query GCF_003946045.1_ASM394604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/reference_markers.fasta -out GCF_003946045.1_ASM394604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:44,454] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:44,457] [INFO] Selected 12 target genomes.
[2024-01-25 20:18:44,457] [INFO] Target genome list was writen to GCF_003946045.1_ASM394604v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:44,475] [INFO] Task started: fastANI
[2024-01-25 20:18:44,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd01c49-4c28-4d2d-b4dd-eb9030a206da/GCF_003946045.1_ASM394604v1_genomic.fna.gz --refList GCF_003946045.1_ASM394604v1_genomic.fna/target_genomes.txt --output GCF_003946045.1_ASM394604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:56,109] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:56,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:56,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:56,118] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:56,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:56,118] [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 mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	100.0	1020	1020	95	conclusive
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	94.1957	899	1020	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	93.0323	887	1020	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	83.8955	714	1020	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	82.9125	601	1020	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	82.8281	595	1020	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	81.966	534	1020	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	80.4945	358	1020	95	below_threshold
Secundilactobacillus paracollinoides	strain=DSM 15502	GCA_001435115.1	240427	240427	type	True	79.3941	90	1020	95	below_threshold
Secundilactobacillus paracollinoides	strain=JCM 11969	GCA_001311135.1	240427	240427	type	True	79.369	95	1020	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	78.3579	89	1020	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	78.2829	86	1020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:56,120] [INFO] DFAST Taxonomy check result was written to GCF_003946045.1_ASM394604v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:56,120] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:56,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:56,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/checkm_data
[2024-01-25 20:18:56,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:56,153] [INFO] Task started: CheckM
[2024-01-25 20:18:56,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946045.1_ASM394604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946045.1_ASM394604v1_genomic.fna/checkm_input GCF_003946045.1_ASM394604v1_genomic.fna/checkm_result
[2024-01-25 20:19:21,721] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:21,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:21,752] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:21,753] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:21,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946045.1_ASM394604v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:21,753] [INFO] Task started: Blastn
[2024-01-25 20:19:21,753] [INFO] Running command: blastn -query GCF_003946045.1_ASM394604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f17dc2-fa08-41ba-9d46-431391677e00/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946045.1_ASM394604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:22,501] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:22,504] [INFO] Selected 8 target genomes.
[2024-01-25 20:19:22,504] [INFO] Target genome list was writen to GCF_003946045.1_ASM394604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:22,510] [INFO] Task started: fastANI
[2024-01-25 20:19:22,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd01c49-4c28-4d2d-b4dd-eb9030a206da/GCF_003946045.1_ASM394604v1_genomic.fna.gz --refList GCF_003946045.1_ASM394604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946045.1_ASM394604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:31,140] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:31,147] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:31,147] [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_003946045.1	s__Levilactobacillus mulengensis	100.0	1020	1020	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_016861585.1	s__Levilactobacillus sp016861585	94.091	876	1020	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_016861655.1	s__Levilactobacillus sp016861655	93.0323	887	1020	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	83.8454	719	1020	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666485.1	s__Levilactobacillus brevis_A	83.1094	645	1020	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946085.1	s__Levilactobacillus angrenensis	82.8648	605	1020	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	82.8282	595	1020	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	81.9832	533	1020	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:31,149] [INFO] GTDB search result was written to GCF_003946045.1_ASM394604v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:31,149] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:31,152] [INFO] DFAST_QC result json was written to GCF_003946045.1_ASM394604v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:31,152] [INFO] DFAST_QC completed!
[2024-01-25 20:19:31,152] [INFO] Total running time: 0h0m56s