[2024-01-24 15:18:18,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,893] [INFO] DQC Reference Directory: /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference
[2024-01-24 15:18:20,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,199] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,199] [INFO] Running command: gunzip -c /var/lib/cwl/stge6a01123-005d-4533-95a9-677a66575434/GCF_005405485.1_ASM540548v1_genomic.fna.gz | prodigal -d GCF_005405485.1_ASM540548v1_genomic.fna/cds.fna -a GCF_005405485.1_ASM540548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:30,800] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:30,800] [INFO] Task started: HMMsearch
[2024-01-24 15:18:30,801] [INFO] Running command: hmmsearch --tblout GCF_005405485.1_ASM540548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/reference_markers.hmm GCF_005405485.1_ASM540548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:31,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:31,143] [INFO] Found 6/6 markers.
[2024-01-24 15:18:31,189] [INFO] Query marker FASTA was written to GCF_005405485.1_ASM540548v1_genomic.fna/markers.fasta
[2024-01-24 15:18:31,189] [INFO] Task started: Blastn
[2024-01-24 15:18:31,189] [INFO] Running command: blastn -query GCF_005405485.1_ASM540548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/reference_markers.fasta -out GCF_005405485.1_ASM540548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:31,841] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:31,845] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:31,846] [INFO] Target genome list was writen to GCF_005405485.1_ASM540548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:31,855] [INFO] Task started: fastANI
[2024-01-24 15:18:31,856] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a01123-005d-4533-95a9-677a66575434/GCF_005405485.1_ASM540548v1_genomic.fna.gz --refList GCF_005405485.1_ASM540548v1_genomic.fna/target_genomes.txt --output GCF_005405485.1_ASM540548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:45,971] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:45,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:45,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:45,989] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:45,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:45,989] [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
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	100.0	1553	1558	95	conclusive
Enterococcus raffinosus	strain=DSM 5633	GCA_001886185.1	71452	71452	type	True	82.3503	840	1558	95	below_threshold
Enterococcus raffinosus	strain=NBRC 100492	GCA_001544115.1	71452	71452	type	True	82.3157	830	1558	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	82.1411	902	1558	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000393875.1	71451	71451	type	True	82.1364	922	1558	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	82.0903	913	1558	95	below_threshold
Enterococcus malodoratus	strain=NCTC12365	GCA_900447955.1	71451	71451	type	True	82.0825	933	1558	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	81.7138	822	1558	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	81.708	796	1558	95	below_threshold
Enterococcus avium	strain=NCTC9938	GCA_900447655.1	33945	33945	type	True	81.667	824	1558	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000406965.1	33945	33945	type	True	81.6616	829	1558	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.9793	98	1558	95	below_threshold
Vagococcus zengguangii	strain=MN-17	GCA_005145005.1	2571750	2571750	type	True	77.6253	55	1558	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	77.6033	84	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:45,992] [INFO] DFAST Taxonomy check result was written to GCF_005405485.1_ASM540548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:45,993] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:45,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:45,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/checkm_data
[2024-01-24 15:18:45,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:46,048] [INFO] Task started: CheckM
[2024-01-24 15:18:46,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405485.1_ASM540548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405485.1_ASM540548v1_genomic.fna/checkm_input GCF_005405485.1_ASM540548v1_genomic.fna/checkm_result
[2024-01-24 15:19:22,434] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:22,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:22,457] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:22,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:22,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405485.1_ASM540548v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:22,459] [INFO] Task started: Blastn
[2024-01-24 15:19:22,459] [INFO] Running command: blastn -query GCF_005405485.1_ASM540548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b8bda8-5c9a-4bd2-a523-02165d686a58/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405485.1_ASM540548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:23,251] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:23,259] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:23,259] [INFO] Target genome list was writen to GCF_005405485.1_ASM540548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:23,272] [INFO] Task started: fastANI
[2024-01-24 15:19:23,272] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a01123-005d-4533-95a9-677a66575434/GCF_005405485.1_ASM540548v1_genomic.fna.gz --refList GCF_005405485.1_ASM540548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405485.1_ASM540548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:35,114] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:35,131] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:35,131] [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_005405485.1	s__Enterococcus_A hulanensis	100.0	1553	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	97.15	97.02	0.83	0.81	4	conclusive
GCF_017315985.1	s__Enterococcus_A sp017315985	83.6921	995	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886185.1	s__Enterococcus_A raffinosus	82.3506	840	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.27	97.96	0.91	0.87	12	-
GCF_000407185.1	s__Enterococcus_A malodoratus	82.0659	916	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.33	98.27	0.94	0.84	8	-
GCF_018917525.1	s__Enterococcus_A raffinosus_A	81.8548	827	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000406965.1	s__Enterococcus_A avium	81.668	827	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	-
GCF_005405205.1	s__Enterococcus_A pingfangensis	81.6342	442	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407545.1	s__Enterococcus_A gilvus	81.4061	687	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.79	97.90	0.91	0.83	8	-
GCF_005405365.1	s__Enterococcus_A xiangfangensis	81.2221	499	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.65	99.31	0.96	0.92	3	-
GCF_005405225.1	s__Enterococcus_A dongliensis	81.152	370	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885905.1	s__Enterococcus_A devriesei	80.5966	549	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.13	98.05	0.88	0.86	3	-
GCF_001885945.1	s__Enterococcus_A hermanniensis	80.1739	389	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706605.1	s__Enterococcus_A sp902706605	78.0068	183	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145005.1	s__Vagococcus_A zengguangii	77.6253	55	1558	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_001886195.1	s__Enterococcus_B ratti	77.6033	84	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:35,134] [INFO] GTDB search result was written to GCF_005405485.1_ASM540548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:35,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:35,139] [INFO] DFAST_QC result json was written to GCF_005405485.1_ASM540548v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:35,139] [INFO] DFAST_QC completed!
[2024-01-24 15:19:35,139] [INFO] Total running time: 0h1m16s