[2024-01-25 19:31:51,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,487] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference
[2024-01-25 19:31:52,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,678] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ff4bf8b-4f0a-4278-8343-6c648668d2c2/GCF_016861695.1_ASM1686169v1_genomic.fna.gz | prodigal -d GCF_016861695.1_ASM1686169v1_genomic.fna/cds.fna -a GCF_016861695.1_ASM1686169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:31:59,389] [INFO] Task succeeded: Prodigal
[2024-01-25 19:31:59,389] [INFO] Task started: HMMsearch
[2024-01-25 19:31:59,389] [INFO] Running command: hmmsearch --tblout GCF_016861695.1_ASM1686169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/reference_markers.hmm GCF_016861695.1_ASM1686169v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:31:59,588] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:31:59,589] [INFO] Found 6/6 markers.
[2024-01-25 19:31:59,613] [INFO] Query marker FASTA was written to GCF_016861695.1_ASM1686169v1_genomic.fna/markers.fasta
[2024-01-25 19:31:59,613] [INFO] Task started: Blastn
[2024-01-25 19:31:59,613] [INFO] Running command: blastn -query GCF_016861695.1_ASM1686169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/reference_markers.fasta -out GCF_016861695.1_ASM1686169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:00,155] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:00,159] [INFO] Selected 15 target genomes.
[2024-01-25 19:32:00,159] [INFO] Target genome list was writen to GCF_016861695.1_ASM1686169v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:00,162] [INFO] Task started: fastANI
[2024-01-25 19:32:00,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff4bf8b-4f0a-4278-8343-6c648668d2c2/GCF_016861695.1_ASM1686169v1_genomic.fna.gz --refList GCF_016861695.1_ASM1686169v1_genomic.fna/target_genomes.txt --output GCF_016861695.1_ASM1686169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:10,496] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:10,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:10,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:10,506] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:10,506] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:10,507] [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 andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	100.0	992	992	95	conclusive
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	90.3783	814	992	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	87.3885	770	992	95	below_threshold
Levilactobacillus fujinensis	strain=218-6	GCA_003946335.1	2486024	2486024	type	True	87.0723	762	992	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	82.0803	526	992	95	below_threshold
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	81.9364	527	992	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	81.8829	462	992	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	81.5906	458	992	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	81.385	501	992	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	81.1449	488	992	95	below_threshold
Secundilactobacillus collinoides	strain=DSM 20515	GCA_001435975.1	33960	33960	type	True	78.8752	99	992	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	78.7973	95	992	95	below_threshold
Lactiplantibacillus herbarum	strain=TCF032-E4	GCA_001039045.1	1670446	1670446	type	True	77.5919	86	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:10,508] [INFO] DFAST Taxonomy check result was written to GCF_016861695.1_ASM1686169v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:10,508] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:10,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:10,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/checkm_data
[2024-01-25 19:32:10,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:10,540] [INFO] Task started: CheckM
[2024-01-25 19:32:10,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861695.1_ASM1686169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861695.1_ASM1686169v1_genomic.fna/checkm_input GCF_016861695.1_ASM1686169v1_genomic.fna/checkm_result
[2024-01-25 19:32:34,859] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:34,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:34,880] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:34,880] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:34,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861695.1_ASM1686169v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:34,881] [INFO] Task started: Blastn
[2024-01-25 19:32:34,881] [INFO] Running command: blastn -query GCF_016861695.1_ASM1686169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3907846-25ee-4f6a-ba26-c9f64d677537/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861695.1_ASM1686169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:35,663] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:35,666] [INFO] Selected 11 target genomes.
[2024-01-25 19:32:35,666] [INFO] Target genome list was writen to GCF_016861695.1_ASM1686169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:35,674] [INFO] Task started: fastANI
[2024-01-25 19:32:35,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff4bf8b-4f0a-4278-8343-6c648668d2c2/GCF_016861695.1_ASM1686169v1_genomic.fna.gz --refList GCF_016861695.1_ASM1686169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861695.1_ASM1686169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:45,208] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:45,215] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:45,216] [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_016861695.1	s__Levilactobacillus sp016861695	100.0	992	992	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_001435525.1	s__Levilactobacillus koreensis	90.3769	814	992	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_007115095.1	s__Levilactobacillus enshiensis	87.3853	770	992	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946335.1	s__Levilactobacillus fujinensis	87.0589	763	992	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	82.0573	527	992	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	81.8808	462	992	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	81.8633	526	992	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_003946085.1	s__Levilactobacillus angrenensis	81.5454	461	992	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	81.4082	499	992	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	81.2567	501	992	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	81.1682	486	992	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 19:32:45,217] [INFO] GTDB search result was written to GCF_016861695.1_ASM1686169v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:45,218] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:45,221] [INFO] DFAST_QC result json was written to GCF_016861695.1_ASM1686169v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:45,221] [INFO] DFAST_QC completed!
[2024-01-25 19:32:45,221] [INFO] Total running time: 0h0m54s