[2024-01-24 13:57:42,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference
[2024-01-24 13:57:43,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,903] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgffdeae73-3718-49d3-b724-8d22b9323b8d/GCF_001433855.1_ASM143385v1_genomic.fna.gz | prodigal -d GCF_001433855.1_ASM143385v1_genomic.fna/cds.fna -a GCF_001433855.1_ASM143385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:49,957] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:49,958] [INFO] Task started: HMMsearch
[2024-01-24 13:57:49,958] [INFO] Running command: hmmsearch --tblout GCF_001433855.1_ASM143385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/reference_markers.hmm GCF_001433855.1_ASM143385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:50,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:50,233] [INFO] Found 6/6 markers.
[2024-01-24 13:57:50,255] [INFO] Query marker FASTA was written to GCF_001433855.1_ASM143385v1_genomic.fna/markers.fasta
[2024-01-24 13:57:50,256] [INFO] Task started: Blastn
[2024-01-24 13:57:50,256] [INFO] Running command: blastn -query GCF_001433855.1_ASM143385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/reference_markers.fasta -out GCF_001433855.1_ASM143385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:50,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:50,853] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:50,853] [INFO] Target genome list was writen to GCF_001433855.1_ASM143385v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:50,858] [INFO] Task started: fastANI
[2024-01-24 13:57:50,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdeae73-3718-49d3-b724-8d22b9323b8d/GCF_001433855.1_ASM143385v1_genomic.fna.gz --refList GCF_001433855.1_ASM143385v1_genomic.fna/target_genomes.txt --output GCF_001433855.1_ASM143385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:58,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:58,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:58,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:58,452] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:57:58,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:58,453] [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 brevis	strain=DSM 20054	GCA_001433855.1	1580	1580	type	True	100.0	819	820	95	conclusive
Levilactobacillus brevis	strain=NCTC13768	GCA_900475625.1	1580	1580	type	True	99.9962	819	820	95	conclusive
Levilactobacillus brevis	strain=ATCC 14869	GCA_000469365.1	1580	1580	type	True	99.9114	775	820	95	conclusive
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	80.3996	299	820	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	80.289	315	820	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	80.2628	295	820	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	80.2254	321	820	95	below_threshold
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	80.1622	330	820	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	80.1465	329	820	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	80.1214	324	820	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	80.0045	327	820	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	77.8009	73	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:58,455] [INFO] DFAST Taxonomy check result was written to GCF_001433855.1_ASM143385v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:58,456] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:58,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:58,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/checkm_data
[2024-01-24 13:57:58,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:58,489] [INFO] Task started: CheckM
[2024-01-24 13:57:58,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001433855.1_ASM143385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001433855.1_ASM143385v1_genomic.fna/checkm_input GCF_001433855.1_ASM143385v1_genomic.fna/checkm_result
[2024-01-24 13:58:24,095] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:24,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:24,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:24,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:24,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001433855.1_ASM143385v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:24,111] [INFO] Task started: Blastn
[2024-01-24 13:58:24,111] [INFO] Running command: blastn -query GCF_001433855.1_ASM143385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70ce17e3-e147-4e23-94e5-f87a815b7ea6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001433855.1_ASM143385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,923] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:24,923] [INFO] Target genome list was writen to GCF_001433855.1_ASM143385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:25,018] [INFO] Task started: fastANI
[2024-01-24 13:58:25,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdeae73-3718-49d3-b724-8d22b9323b8d/GCF_001433855.1_ASM143385v1_genomic.fna.gz --refList GCF_001433855.1_ASM143385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001433855.1_ASM143385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:33,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:33,702] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:33,703] [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_001433855.1	s__Levilactobacillus brevis	100.0	819	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	97.91	96.65	0.91	0.84	85	conclusive
GCF_012641185.1	s__Levilactobacillus sp012641185	80.3996	299	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	-
GCF_003946265.1	s__Levilactobacillus yonginensis	80.3402	297	820	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	80.2892	315	820	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	80.2431	296	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001434395.1	s__Levilactobacillus hammesii	80.2362	280	820	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	80.2074	322	820	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	80.1633	328	820	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	80.1608	331	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_003946335.1	s__Levilactobacillus fujinensis	80.1229	286	820	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	80.1214	324	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946345.1	s__Levilactobacillus tongjiangensis	80.0498	307	820	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	80.0332	337	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_007115095.1	s__Levilactobacillus enshiensis	80.0045	327	820	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	79.9809	305	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434055.1	s__Levilactobacillus parabrevis	79.817	277	820	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.99	99.98	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,704] [INFO] GTDB search result was written to GCF_001433855.1_ASM143385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:33,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:33,709] [INFO] DFAST_QC result json was written to GCF_001433855.1_ASM143385v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:33,710] [INFO] DFAST_QC completed!
[2024-01-24 13:58:33,710] [INFO] Total running time: 0h0m51s