[2024-01-25 19:01:05,580] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:05,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:05,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference
[2024-01-25 19:01:06,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:06,713] [INFO] Task started: Prodigal
[2024-01-25 19:01:06,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg36d7e674-2381-40f4-88ea-6065899f79d8/GCF_016861605.1_ASM1686160v1_genomic.fna.gz | prodigal -d GCF_016861605.1_ASM1686160v1_genomic.fna/cds.fna -a GCF_016861605.1_ASM1686160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:13,714] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:13,715] [INFO] Task started: HMMsearch
[2024-01-25 19:01:13,715] [INFO] Running command: hmmsearch --tblout GCF_016861605.1_ASM1686160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/reference_markers.hmm GCF_016861605.1_ASM1686160v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:13,907] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:13,909] [INFO] Found 6/6 markers.
[2024-01-25 19:01:13,933] [INFO] Query marker FASTA was written to GCF_016861605.1_ASM1686160v1_genomic.fna/markers.fasta
[2024-01-25 19:01:13,933] [INFO] Task started: Blastn
[2024-01-25 19:01:13,933] [INFO] Running command: blastn -query GCF_016861605.1_ASM1686160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/reference_markers.fasta -out GCF_016861605.1_ASM1686160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:14,495] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:14,498] [INFO] Selected 12 target genomes.
[2024-01-25 19:01:14,498] [INFO] Target genome list was writen to GCF_016861605.1_ASM1686160v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:14,503] [INFO] Task started: fastANI
[2024-01-25 19:01:14,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg36d7e674-2381-40f4-88ea-6065899f79d8/GCF_016861605.1_ASM1686160v1_genomic.fna.gz --refList GCF_016861605.1_ASM1686160v1_genomic.fna/target_genomes.txt --output GCF_016861605.1_ASM1686160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:25,324] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:25,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:25,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:25,332] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:01:25,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:01:25,332] [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 wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	100.0	1011	1018	95	conclusive
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	94.252	913	1018	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	93.829	888	1018	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	84.0009	699	1018	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	83.1004	594	1018	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	82.8442	605	1018	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	82.0504	523	1018	95	below_threshold
Lactiplantibacillus pentosus	strain=ATCC 8041	GCA_004354685.1	1589	1589	type	True	78.4213	85	1018	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	78.3847	86	1018	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	78.2395	85	1018	95	below_threshold
Lactiplantibacillus herbarum	strain=TCF032-E4	GCA_001039045.1	1670446	1670446	type	True	77.9617	67	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:25,334] [INFO] DFAST Taxonomy check result was written to GCF_016861605.1_ASM1686160v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:25,335] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:25,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:25,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/checkm_data
[2024-01-25 19:01:25,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:25,367] [INFO] Task started: CheckM
[2024-01-25 19:01:25,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861605.1_ASM1686160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861605.1_ASM1686160v1_genomic.fna/checkm_input GCF_016861605.1_ASM1686160v1_genomic.fna/checkm_result
[2024-01-25 19:01:50,988] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:50,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:51,005] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:51,005] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:51,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861605.1_ASM1686160v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:51,006] [INFO] Task started: Blastn
[2024-01-25 19:01:51,006] [INFO] Running command: blastn -query GCF_016861605.1_ASM1686160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8a800b-9722-4b98-88e9-0ab0cc4e80bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861605.1_ASM1686160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:51,789] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:51,792] [INFO] Selected 8 target genomes.
[2024-01-25 19:01:51,792] [INFO] Target genome list was writen to GCF_016861605.1_ASM1686160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:51,803] [INFO] Task started: fastANI
[2024-01-25 19:01:51,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg36d7e674-2381-40f4-88ea-6065899f79d8/GCF_016861605.1_ASM1686160v1_genomic.fna.gz --refList GCF_016861605.1_ASM1686160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861605.1_ASM1686160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:00,412] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:00,419] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:00,419] [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_016861585.1	s__Levilactobacillus sp016861585	99.8755	957	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	conclusive
GCF_003946045.1	s__Levilactobacillus mulengensis	94.252	913	1018	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	93.8483	887	1018	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	83.9341	704	1018	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	83.0864	595	1018	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	82.8876	638	1018	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	82.8581	604	1018	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	82.0501	523	1018	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 19:02:00,421] [INFO] GTDB search result was written to GCF_016861605.1_ASM1686160v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:00,421] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:00,423] [INFO] DFAST_QC result json was written to GCF_016861605.1_ASM1686160v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:00,424] [INFO] DFAST_QC completed!
[2024-01-25 19:02:00,424] [INFO] Total running time: 0h0m55s