[2024-01-25 20:14:35,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:35,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:35,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference
[2024-01-25 20:14:36,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:36,686] [INFO] Task started: Prodigal
[2024-01-25 20:14:36,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf00a8b-cb19-4e5d-b937-8a278cd294bc/GCF_001437085.1_ASM143708v1_genomic.fna.gz | prodigal -d GCF_001437085.1_ASM143708v1_genomic.fna/cds.fna -a GCF_001437085.1_ASM143708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:41,010] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:41,010] [INFO] Task started: HMMsearch
[2024-01-25 20:14:41,010] [INFO] Running command: hmmsearch --tblout GCF_001437085.1_ASM143708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/reference_markers.hmm GCF_001437085.1_ASM143708v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:41,205] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:41,206] [INFO] Found 6/6 markers.
[2024-01-25 20:14:41,229] [INFO] Query marker FASTA was written to GCF_001437085.1_ASM143708v1_genomic.fna/markers.fasta
[2024-01-25 20:14:41,229] [INFO] Task started: Blastn
[2024-01-25 20:14:41,229] [INFO] Running command: blastn -query GCF_001437085.1_ASM143708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/reference_markers.fasta -out GCF_001437085.1_ASM143708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:41,783] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:41,786] [INFO] Selected 17 target genomes.
[2024-01-25 20:14:41,786] [INFO] Target genome list was writen to GCF_001437085.1_ASM143708v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:41,794] [INFO] Task started: fastANI
[2024-01-25 20:14:41,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf00a8b-cb19-4e5d-b937-8a278cd294bc/GCF_001437085.1_ASM143708v1_genomic.fna.gz --refList GCF_001437085.1_ASM143708v1_genomic.fna/target_genomes.txt --output GCF_001437085.1_ASM143708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:49,910] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:49,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:49,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:49,918] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:14:49,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:49,919] [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
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	100.0	854	854	95	conclusive
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	99.9977	853	854	95	conclusive
Carnobacterium divergens	strain=66	GCA_000744255.1	2748	2748	type	True	99.9975	853	854	95	conclusive
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	79.0858	305	854	95	below_threshold
Carnobacterium maltaromaticum	strain=DSM 20342	GCA_001437315.1	2751	2751	type	True	78.9728	306	854	95	below_threshold
Carnobacterium maltaromaticum	strain=MX5	GCA_000744945.1	2751	2751	type	True	78.9402	319	854	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	78.1161	117	854	95	below_threshold
Carnobacterium mobile	strain=MT37L	GCA_000744825.1	2750	2750	type	True	77.7785	114	854	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	77.5949	114	854	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	77.5199	133	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:49,920] [INFO] DFAST Taxonomy check result was written to GCF_001437085.1_ASM143708v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:49,922] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:49,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:49,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/checkm_data
[2024-01-25 20:14:49,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:49,951] [INFO] Task started: CheckM
[2024-01-25 20:14:49,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001437085.1_ASM143708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001437085.1_ASM143708v1_genomic.fna/checkm_input GCF_001437085.1_ASM143708v1_genomic.fna/checkm_result
[2024-01-25 20:15:09,337] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:09,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:09,359] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:09,360] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:09,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001437085.1_ASM143708v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:09,360] [INFO] Task started: Blastn
[2024-01-25 20:15:09,360] [INFO] Running command: blastn -query GCF_001437085.1_ASM143708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bee7ded-3f8f-4510-acd3-5bece41f0756/dqc_reference/reference_markers_gtdb.fasta -out GCF_001437085.1_ASM143708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:10,123] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:10,126] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:10,126] [INFO] Target genome list was writen to GCF_001437085.1_ASM143708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:10,137] [INFO] Task started: fastANI
[2024-01-25 20:15:10,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf00a8b-cb19-4e5d-b937-8a278cd294bc/GCF_001437085.1_ASM143708v1_genomic.fna.gz --refList GCF_001437085.1_ASM143708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001437085.1_ASM143708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:17,272] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:17,280] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:17,281] [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_000744255.1	s__Carnobacterium divergens	99.9975	853	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	conclusive
GCF_900258435.1	s__Carnobacterium divergens_A	94.1689	756	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.21	98.87	0.95	0.92	17	-
GCF_000744375.1	s__Carnobacterium gallinarum	79.0863	305	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744945.1	s__Carnobacterium maltaromaticum	78.9533	318	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	98.15	96.42	0.90	0.81	35	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	78.1161	117	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	-
GCF_900111355.1	s__Isobaculum melis	78.0729	141	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Isobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145005.1	s__Vagococcus_A zengguangii	77.8686	52	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.48	99.48	0.96	0.96	2	-
GCF_000744825.1	s__Carnobacterium_A mobile	77.7785	114	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	97.99	97.99	0.87	0.87	2	-
GCF_000195575.1	s__Carnobacterium_A sp000195575	77.7523	105	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377505.1	s__Enterococcus sp017377505	77.6219	92	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_900102725.1	s__Carnobacterium_A viridans	77.567	115	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_900177385.1	s__Carnobacterium_A iners	77.5415	112	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000746825.1	s__Carnobacterium_A inhibens	77.5199	133	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:17,282] [INFO] GTDB search result was written to GCF_001437085.1_ASM143708v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:17,282] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:17,285] [INFO] DFAST_QC result json was written to GCF_001437085.1_ASM143708v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:17,285] [INFO] DFAST_QC completed!
[2024-01-25 20:15:17,286] [INFO] Total running time: 0h0m42s