[2024-01-25 18:28:50,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference
[2024-01-25 18:28:51,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,669] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,669] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0c07067-4396-4eeb-8f9a-5df10bc46a9f/GCF_001433995.1_ASM143399v1_genomic.fna.gz | prodigal -d GCF_001433995.1_ASM143399v1_genomic.fna/cds.fna -a GCF_001433995.1_ASM143399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:57,147] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:57,147] [INFO] Task started: HMMsearch
[2024-01-25 18:28:57,147] [INFO] Running command: hmmsearch --tblout GCF_001433995.1_ASM143399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/reference_markers.hmm GCF_001433995.1_ASM143399v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:57,331] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:57,333] [INFO] Found 6/6 markers.
[2024-01-25 18:28:57,356] [INFO] Query marker FASTA was written to GCF_001433995.1_ASM143399v1_genomic.fna/markers.fasta
[2024-01-25 18:28:57,356] [INFO] Task started: Blastn
[2024-01-25 18:28:57,356] [INFO] Running command: blastn -query GCF_001433995.1_ASM143399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/reference_markers.fasta -out GCF_001433995.1_ASM143399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:57,897] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:57,900] [INFO] Selected 27 target genomes.
[2024-01-25 18:28:57,900] [INFO] Target genome list was writen to GCF_001433995.1_ASM143399v1_genomic.fna/target_genomes.txt
[2024-01-25 18:28:57,918] [INFO] Task started: fastANI
[2024-01-25 18:28:57,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c07067-4396-4eeb-8f9a-5df10bc46a9f/GCF_001433995.1_ASM143399v1_genomic.fna.gz --refList GCF_001433995.1_ASM143399v1_genomic.fna/target_genomes.txt --output GCF_001433995.1_ASM143399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:10,329] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:10,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:10,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:10,340] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:29:10,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:10,340] [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
Secundilactobacillus kimchicus	strain=JCM 15530	GCA_001433995.1	528209	528209	type	True	100.0	847	848	95	conclusive
Secundilactobacillus odoratitofui	strain=DSM 19909	GCA_001434895.1	480930	480930	type	True	78.3409	131	848	95	below_threshold
Levilactobacillus fujinensis	strain=218-6	GCA_003946335.1	2486024	2486024	type	True	78.3166	53	848	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	78.2559	129	848	95	below_threshold
Secundilactobacillus similis	strain=DSM 23365	GCA_001436595.1	414682	414682	type	True	78.214	132	848	95	below_threshold
Secundilactobacillus similis	strain=JCM 2765	GCA_001311075.1	414682	414682	type	True	78.2036	129	848	95	below_threshold
Secundilactobacillus silagincola	strain=IWT5	GCA_002583405.1	1714681	1714681	type	True	78.1133	103	848	95	below_threshold
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	78.0322	113	848	95	below_threshold
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	77.9792	115	848	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.9321	117	848	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	77.8343	113	848	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	77.7561	59	848	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	77.7355	119	848	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	77.6747	58	848	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	77.5458	58	848	95	below_threshold
Lactiplantibacillus pentosus	strain=ATCC 8041	GCA_004354685.1	1589	1589	type	True	77.5377	60	848	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	77.3994	60	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:10,342] [INFO] DFAST Taxonomy check result was written to GCF_001433995.1_ASM143399v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:10,342] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:10,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:10,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/checkm_data
[2024-01-25 18:29:10,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:10,370] [INFO] Task started: CheckM
[2024-01-25 18:29:10,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001433995.1_ASM143399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001433995.1_ASM143399v1_genomic.fna/checkm_input GCF_001433995.1_ASM143399v1_genomic.fna/checkm_result
[2024-01-25 18:29:31,924] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:31,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:31,941] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:31,941] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:31,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001433995.1_ASM143399v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:31,942] [INFO] Task started: Blastn
[2024-01-25 18:29:31,942] [INFO] Running command: blastn -query GCF_001433995.1_ASM143399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c828529-ea28-41f1-89c0-6a64e3f7c702/dqc_reference/reference_markers_gtdb.fasta -out GCF_001433995.1_ASM143399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:32,652] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:32,655] [INFO] Selected 26 target genomes.
[2024-01-25 18:29:32,655] [INFO] Target genome list was writen to GCF_001433995.1_ASM143399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:32,678] [INFO] Task started: fastANI
[2024-01-25 18:29:32,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0c07067-4396-4eeb-8f9a-5df10bc46a9f/GCF_001433995.1_ASM143399v1_genomic.fna.gz --refList GCF_001433995.1_ASM143399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001433995.1_ASM143399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:45,053] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:45,063] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:45,063] [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_001433995.1	s__Secundilactobacillus kimchicus	100.0	847	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.61	99.40	0.97	0.95	3	conclusive
GCF_001434895.1	s__Secundilactobacillus odoratitofui	78.3622	129	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.87	99.87	1.00	1.00	2	-
GCF_003946335.1	s__Levilactobacillus fujinensis	78.3166	53	848	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	78.2134	54	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311075.1	s__Secundilactobacillus similis	78.2036	129	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.93	99.93	0.98	0.98	2	-
GCF_002583405.1	s__Secundilactobacillus silagincola	78.1133	103	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_001435095.1	s__Levilactobacillus spicheri	78.1051	51	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	-
GCF_007115095.1	s__Levilactobacillus enshiensis	78.0356	52	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435975.1	s__Secundilactobacillus collinoides	77.9829	118	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.82	99.79	0.97	0.94	3	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	77.9792	115	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311135.1	s__Secundilactobacillus paracollinoides	77.9355	114	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.57	99.45	0.95	0.89	5	-
GCF_002217945.1	s__Secundilactobacillus silagei	77.8343	113	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	77.7864	58	848	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	77.7561	59	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641075.1	s__Secundilactobacillus sp012641075	77.7355	119	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	77.6747	58	848	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 18:29:45,065] [INFO] GTDB search result was written to GCF_001433995.1_ASM143399v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:45,066] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:45,069] [INFO] DFAST_QC result json was written to GCF_001433995.1_ASM143399v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:45,069] [INFO] DFAST_QC completed!
[2024-01-25 18:29:45,069] [INFO] Total running time: 0h0m55s