[2024-01-24 11:18:04,573] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference
[2024-01-24 11:18:05,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:05,761] [INFO] Task started: Prodigal
[2024-01-24 11:18:05,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cde0223-05a0-40ba-bdd2-1949bd229c93/GCF_003946085.1_ASM394608v1_genomic.fna.gz | prodigal -d GCF_003946085.1_ASM394608v1_genomic.fna/cds.fna -a GCF_003946085.1_ASM394608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:13,041] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:13,041] [INFO] Task started: HMMsearch
[2024-01-24 11:18:13,041] [INFO] Running command: hmmsearch --tblout GCF_003946085.1_ASM394608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/reference_markers.hmm GCF_003946085.1_ASM394608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:13,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:13,275] [INFO] Found 6/6 markers.
[2024-01-24 11:18:13,300] [INFO] Query marker FASTA was written to GCF_003946085.1_ASM394608v1_genomic.fna/markers.fasta
[2024-01-24 11:18:13,301] [INFO] Task started: Blastn
[2024-01-24 11:18:13,301] [INFO] Running command: blastn -query GCF_003946085.1_ASM394608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/reference_markers.fasta -out GCF_003946085.1_ASM394608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:13,875] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:13,879] [INFO] Selected 11 target genomes.
[2024-01-24 11:18:13,880] [INFO] Target genome list was writen to GCF_003946085.1_ASM394608v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:13,966] [INFO] Task started: fastANI
[2024-01-24 11:18:13,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cde0223-05a0-40ba-bdd2-1949bd229c93/GCF_003946085.1_ASM394608v1_genomic.fna.gz --refList GCF_003946085.1_ASM394608v1_genomic.fna/target_genomes.txt --output GCF_003946085.1_ASM394608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:22,788] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:22,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:22,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:22,801] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:18:22,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:22,802] [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	100.0	896	898	95	conclusive
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	87.7799	725	898	95	below_threshold
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	83.0125	608	898	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	82.9899	599	898	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	82.9276	609	898	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	82.4854	574	898	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	81.4903	424	898	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	81.2112	459	898	95	below_threshold
Secundilactobacillus oryzae	strain=JCM 18671	GCA_001311525.1	1202668	1202668	type	True	79.0906	71	898	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	78.0926	95	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:22,803] [INFO] DFAST Taxonomy check result was written to GCF_003946085.1_ASM394608v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:22,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:22,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:22,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/checkm_data
[2024-01-24 11:18:22,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:22,836] [INFO] Task started: CheckM
[2024-01-24 11:18:22,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946085.1_ASM394608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946085.1_ASM394608v1_genomic.fna/checkm_input GCF_003946085.1_ASM394608v1_genomic.fna/checkm_result
[2024-01-24 11:18:50,052] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:50,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:50,073] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:50,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:50,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946085.1_ASM394608v1_genomic.fna/markers.fasta)
[2024-01-24 11:18:50,074] [INFO] Task started: Blastn
[2024-01-24 11:18:50,075] [INFO] Running command: blastn -query GCF_003946085.1_ASM394608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9da61e10-b4df-49ca-8506-5c824ffea867/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946085.1_ASM394608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:50,844] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:50,848] [INFO] Selected 7 target genomes.
[2024-01-24 11:18:50,848] [INFO] Target genome list was writen to GCF_003946085.1_ASM394608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:50,878] [INFO] Task started: fastANI
[2024-01-24 11:18:50,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cde0223-05a0-40ba-bdd2-1949bd229c93/GCF_003946085.1_ASM394608v1_genomic.fna.gz --refList GCF_003946085.1_ASM394608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946085.1_ASM394608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:18:58,401] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:58,412] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:18:58,412] [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_003946085.1	s__Levilactobacillus angrenensis	100.0	896	898	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_004745505.1	s__Levilactobacillus suantsaiihabitans	87.7763	725	898	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	87.759	728	898	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	83.0935	585	898	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	82.9751	600	898	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	82.9177	610	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007115095.1	s__Levilactobacillus enshiensis	81.4569	427	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:18:58,414] [INFO] GTDB search result was written to GCF_003946085.1_ASM394608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:18:58,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:18:58,418] [INFO] DFAST_QC result json was written to GCF_003946085.1_ASM394608v1_genomic.fna/dqc_result.json
[2024-01-24 11:18:58,418] [INFO] DFAST_QC completed!
[2024-01-24 11:18:58,418] [INFO] Total running time: 0h0m54s