[2024-01-24 12:00:36,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference
[2024-01-24 12:00:39,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,381] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg7983d0b6-9c1c-488e-bc89-2b88981abbd9/GCF_003124125.1_ASM312412v1_genomic.fna.gz | prodigal -d GCF_003124125.1_ASM312412v1_genomic.fna/cds.fna -a GCF_003124125.1_ASM312412v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:43,723] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:43,724] [INFO] Task started: HMMsearch
[2024-01-24 12:00:43,724] [INFO] Running command: hmmsearch --tblout GCF_003124125.1_ASM312412v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/reference_markers.hmm GCF_003124125.1_ASM312412v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:43,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:43,948] [INFO] Found 6/6 markers.
[2024-01-24 12:00:43,970] [INFO] Query marker FASTA was written to GCF_003124125.1_ASM312412v1_genomic.fna/markers.fasta
[2024-01-24 12:00:43,971] [INFO] Task started: Blastn
[2024-01-24 12:00:43,971] [INFO] Running command: blastn -query GCF_003124125.1_ASM312412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/reference_markers.fasta -out GCF_003124125.1_ASM312412v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,176] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,181] [INFO] Selected 23 target genomes.
[2024-01-24 12:00:45,181] [INFO] Target genome list was writen to GCF_003124125.1_ASM312412v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:45,286] [INFO] Task started: fastANI
[2024-01-24 12:00:45,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg7983d0b6-9c1c-488e-bc89-2b88981abbd9/GCF_003124125.1_ASM312412v1_genomic.fna.gz --refList GCF_003124125.1_ASM312412v1_genomic.fna/target_genomes.txt --output GCF_003124125.1_ASM312412v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:53,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:53,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:53,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:53,733] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:53,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:53,734] [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 bambusae	strain=BS-W1	GCA_003124125.1	2024736	2024736	type	True	100.0	635	635	95	conclusive
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	78.2786	61	635	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	77.9585	62	635	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	77.7107	68	635	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	77.67	73	635	95	below_threshold
Levilactobacillus tangyuanensis	strain=137-3	GCA_003946545.1	2486021	2486021	type	True	77.6331	71	635	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	77.4833	73	635	95	below_threshold
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	77.4631	69	635	95	below_threshold
Secundilactobacillus similis	strain=DSM 23365	GCA_001436595.1	414682	414682	type	True	76.9355	55	635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:53,735] [INFO] DFAST Taxonomy check result was written to GCF_003124125.1_ASM312412v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:53,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:53,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:53,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/checkm_data
[2024-01-24 12:00:53,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:53,763] [INFO] Task started: CheckM
[2024-01-24 12:00:53,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003124125.1_ASM312412v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003124125.1_ASM312412v1_genomic.fna/checkm_input GCF_003124125.1_ASM312412v1_genomic.fna/checkm_result
[2024-01-24 12:01:13,434] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:13,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:13,457] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:13,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:13,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003124125.1_ASM312412v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:13,458] [INFO] Task started: Blastn
[2024-01-24 12:01:13,459] [INFO] Running command: blastn -query GCF_003124125.1_ASM312412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dc1bf15-367d-4473-be24-0472a3dcefce/dqc_reference/reference_markers_gtdb.fasta -out GCF_003124125.1_ASM312412v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:14,193] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:14,198] [INFO] Selected 29 target genomes.
[2024-01-24 12:01:14,198] [INFO] Target genome list was writen to GCF_003124125.1_ASM312412v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:14,219] [INFO] Task started: fastANI
[2024-01-24 12:01:14,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg7983d0b6-9c1c-488e-bc89-2b88981abbd9/GCF_003124125.1_ASM312412v1_genomic.fna.gz --refList GCF_003124125.1_ASM312412v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003124125.1_ASM312412v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:25,541] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:25,556] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:25,557] [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_003124125.1	s__Levilactobacillus bambusae	100.0	635	635	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_016861695.1	s__Levilactobacillus sp016861695	78.2786	61	635	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	78.0852	60	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641095.1	s__Levilactobacillus sp012641095	78.006	62	635	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	77.9585	62	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003666485.1	s__Levilactobacillus brevis_A	77.8832	62	635	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	77.7107	68	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946045.1	s__Levilactobacillus mulengensis	77.67	73	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946545.1	s__Levilactobacillus tangyuanensis	77.6331	71	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946265.1	s__Levilactobacillus yonginensis	77.5642	75	635	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	77.4859	69	635	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	77.4833	73	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	77.3717	65	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592085.1	s__Levilactobacillus senmaizukei	77.3597	61	635	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:25,558] [INFO] GTDB search result was written to GCF_003124125.1_ASM312412v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:25,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:25,562] [INFO] DFAST_QC result json was written to GCF_003124125.1_ASM312412v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:25,562] [INFO] DFAST_QC completed!
[2024-01-24 12:01:25,562] [INFO] Total running time: 0h0m49s