[2023-06-12 23:45:45,331] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:45:45,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:45:45,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference
[2023-06-12 23:45:47,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:45:47,572] [INFO] Task started: Prodigal
[2023-06-12 23:45:47,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg448fe76e-ee86-42c1-88cd-02af8619d275/GCA_022776505.1_ASM2277650v1_genomic.fna.gz | prodigal -d GCA_022776505.1_ASM2277650v1_genomic.fna/cds.fna -a GCA_022776505.1_ASM2277650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:45:51,450] [INFO] Task succeeded: Prodigal
[2023-06-12 23:45:51,450] [INFO] Task started: HMMsearch
[2023-06-12 23:45:51,450] [INFO] Running command: hmmsearch --tblout GCA_022776505.1_ASM2277650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/reference_markers.hmm GCA_022776505.1_ASM2277650v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:45:51,692] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:45:51,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg448fe76e-ee86-42c1-88cd-02af8619d275/GCA_022776505.1_ASM2277650v1_genomic.fna.gz]
[2023-06-12 23:45:51,719] [INFO] Query marker FASTA was written to GCA_022776505.1_ASM2277650v1_genomic.fna/markers.fasta
[2023-06-12 23:45:51,719] [INFO] Task started: Blastn
[2023-06-12 23:45:51,719] [INFO] Running command: blastn -query GCA_022776505.1_ASM2277650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/reference_markers.fasta -out GCA_022776505.1_ASM2277650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:45:53,362] [INFO] Task succeeded: Blastn
[2023-06-12 23:45:53,369] [INFO] Selected 18 target genomes.
[2023-06-12 23:45:53,369] [INFO] Target genome list was writen to GCA_022776505.1_ASM2277650v1_genomic.fna/target_genomes.txt
[2023-06-12 23:45:53,386] [INFO] Task started: fastANI
[2023-06-12 23:45:53,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg448fe76e-ee86-42c1-88cd-02af8619d275/GCA_022776505.1_ASM2277650v1_genomic.fna.gz --refList GCA_022776505.1_ASM2277650v1_genomic.fna/target_genomes.txt --output GCA_022776505.1_ASM2277650v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:45:59,350] [INFO] Task succeeded: fastANI
[2023-06-12 23:45:59,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:45:59,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:45:59,364] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:45:59,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:45:59,364] [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
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	82.87	291	503	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	82.4075	285	503	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	82.3963	285	503	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	82.2893	295	503	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	82.2475	296	503	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	82.2132	296	503	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	81.6653	280	503	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	81.4451	332	503	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	81.4058	333	503	95	below_threshold
Streptococcus equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	81.3538	300	503	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	81.2911	304	503	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.8551	92	503	95	below_threshold
Streptococcus uberis	strain=NCTC3858	GCA_900475595.1	1349	1349	type	True	78.7314	94	503	95	below_threshold
Streptococcus halichoeri	strain=CCUG48324	GCA_009870755.1	254785	254785	type	True	78.5098	73	503	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:45:59,367] [INFO] DFAST Taxonomy check result was written to GCA_022776505.1_ASM2277650v1_genomic.fna/tc_result.tsv
[2023-06-12 23:45:59,368] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:45:59,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:45:59,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/checkm_data
[2023-06-12 23:45:59,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:45:59,393] [INFO] Task started: CheckM
[2023-06-12 23:45:59,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022776505.1_ASM2277650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022776505.1_ASM2277650v1_genomic.fna/checkm_input GCA_022776505.1_ASM2277650v1_genomic.fna/checkm_result
[2023-06-12 23:46:20,172] [INFO] Task succeeded: CheckM
[2023-06-12 23:46:20,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:46:20,198] [INFO] ===== Completeness check finished =====
[2023-06-12 23:46:20,199] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:46:20,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022776505.1_ASM2277650v1_genomic.fna/markers.fasta)
[2023-06-12 23:46:20,200] [INFO] Task started: Blastn
[2023-06-12 23:46:20,200] [INFO] Running command: blastn -query GCA_022776505.1_ASM2277650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2692862-5ae3-41de-956a-43237c0995e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022776505.1_ASM2277650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:46:21,106] [INFO] Task succeeded: Blastn
[2023-06-12 23:46:21,112] [INFO] Selected 11 target genomes.
[2023-06-12 23:46:21,112] [INFO] Target genome list was writen to GCA_022776505.1_ASM2277650v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:46:21,119] [INFO] Task started: fastANI
[2023-06-12 23:46:21,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg448fe76e-ee86-42c1-88cd-02af8619d275/GCA_022776505.1_ASM2277650v1_genomic.fna.gz --refList GCA_022776505.1_ASM2277650v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022776505.1_ASM2277650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:46:25,601] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:25,614] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:46:25,614] [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_012277075.1	s__Streptococcus alactolyticus	98.8061	453	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.29	98.88	0.94	0.83	11	conclusive
GCF_900475675.1	s__Streptococcus lutetiensis	82.4364	285	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_000154985.1	s__Streptococcus infantarius	82.2388	295	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCA_000283635.1	s__Streptococcus macedonicus	81.9327	318	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_016461705.1	s__Streptococcus vicugnae	81.6393	281	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_900101445.1	s__Streptococcus equinus_B	81.5967	296	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_002000985.1	s__Streptococcus gallolyticus	81.4506	333	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	81.4415	304	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_900104225.1	s__Streptococcus equinus_D	81.3463	305	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900478025.1	s__Streptococcus pasteurianus	81.1092	319	503	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
--------------------------------------------------------------------------------
[2023-06-12 23:46:25,616] [INFO] GTDB search result was written to GCA_022776505.1_ASM2277650v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:46:25,617] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:46:25,620] [INFO] DFAST_QC result json was written to GCA_022776505.1_ASM2277650v1_genomic.fna/dqc_result.json
[2023-06-12 23:46:25,621] [INFO] DFAST_QC completed!
[2023-06-12 23:46:25,621] [INFO] Total running time: 0h0m40s