[2024-01-25 20:20:50,440] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:50,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:50,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference
[2024-01-25 20:20:51,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:51,607] [INFO] Task started: Prodigal
[2024-01-25 20:20:51,608] [INFO] Running command: gunzip -c /var/lib/cwl/stgd91042e0-d7fb-4acc-9170-12c91c250c3e/GCF_025447695.1_ASM2544769v1_genomic.fna.gz | prodigal -d GCF_025447695.1_ASM2544769v1_genomic.fna/cds.fna -a GCF_025447695.1_ASM2544769v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:54,700] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:54,700] [INFO] Task started: HMMsearch
[2024-01-25 20:20:54,700] [INFO] Running command: hmmsearch --tblout GCF_025447695.1_ASM2544769v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/reference_markers.hmm GCF_025447695.1_ASM2544769v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:54,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:54,898] [INFO] Found 6/6 markers.
[2024-01-25 20:20:54,916] [INFO] Query marker FASTA was written to GCF_025447695.1_ASM2544769v1_genomic.fna/markers.fasta
[2024-01-25 20:20:54,916] [INFO] Task started: Blastn
[2024-01-25 20:20:54,916] [INFO] Running command: blastn -query GCF_025447695.1_ASM2544769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/reference_markers.fasta -out GCF_025447695.1_ASM2544769v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:55,521] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:55,525] [INFO] Selected 27 target genomes.
[2024-01-25 20:20:55,526] [INFO] Target genome list was writen to GCF_025447695.1_ASM2544769v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:55,544] [INFO] Task started: fastANI
[2024-01-25 20:20:55,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91042e0-d7fb-4acc-9170-12c91c250c3e/GCF_025447695.1_ASM2544769v1_genomic.fna.gz --refList GCF_025447695.1_ASM2544769v1_genomic.fna/target_genomes.txt --output GCF_025447695.1_ASM2544769v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:04,154] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:04,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:04,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:04,165] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:04,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:04,166] [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 danieliae	strain=DSM 22233	GCA_025447695.1	747656	747656	type	True	99.9999	461	469	95	conclusive
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	79.0444	66	469	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	79.035	70	469	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9623	63	469	95	below_threshold
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	78.9272	65	469	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	78.9204	66	469	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	78.8886	64	469	95	below_threshold
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	78.7964	63	469	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	78.7761	61	469	95	below_threshold
Streptococcus gordonii	strain=NCTC7865	GCA_900475015.1	1302	1302	suspected-type	True	78.6146	64	469	95	below_threshold
Streptococcus gordonii	strain=ATCC 10558	GCA_001469295.1	1302	1302	suspected-type	True	78.5679	62	469	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	78.5574	68	469	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.5282	65	469	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	78.4392	69	469	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	78.2781	67	469	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	77.9827	65	469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:04,168] [INFO] DFAST Taxonomy check result was written to GCF_025447695.1_ASM2544769v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:04,168] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:04,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:04,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/checkm_data
[2024-01-25 20:21:04,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:04,196] [INFO] Task started: CheckM
[2024-01-25 20:21:04,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025447695.1_ASM2544769v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025447695.1_ASM2544769v1_genomic.fna/checkm_input GCF_025447695.1_ASM2544769v1_genomic.fna/checkm_result
[2024-01-25 20:21:19,877] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:19,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:19,897] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:19,897] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:19,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025447695.1_ASM2544769v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:19,898] [INFO] Task started: Blastn
[2024-01-25 20:21:19,898] [INFO] Running command: blastn -query GCF_025447695.1_ASM2544769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2be7261-59d3-4c2f-8bae-a2f3dff3f5cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_025447695.1_ASM2544769v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:20,702] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:20,706] [INFO] Selected 16 target genomes.
[2024-01-25 20:21:20,706] [INFO] Target genome list was writen to GCF_025447695.1_ASM2544769v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:20,729] [INFO] Task started: fastANI
[2024-01-25 20:21:20,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgd91042e0-d7fb-4acc-9170-12c91c250c3e/GCF_025447695.1_ASM2544769v1_genomic.fna.gz --refList GCF_025447695.1_ASM2544769v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025447695.1_ASM2544769v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:26,387] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:26,396] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:26,396] [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_009767945.1	s__Streptococcus danieliae	97.888	385	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.97	96.46	0.85	0.83	4	conclusive
GCF_013415245.1	s__Streptococcus danieliae_A	93.8073	375	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004570525.1	s__Streptococcus sp004570525	81.5355	264	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016458205.1	s__Streptococcus sp016458205	81.3553	280	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.47	97.40	0.88	0.88	3	-
GCF_000314795.2	s__Streptococcus sp000314795	79.4594	65	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001070715.1	s__Streptococcus pseudopneumoniae_H	78.8007	67	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595525.1	s__Streptococcus respiraculi	78.7761	61	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016648925.1	s__Streptococcus sp900766505	78.7682	67	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	-
GCA_000430305.1	s__Streptococcus mitis_AW	78.6655	68	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0354	95.13	95.13	0.89	0.89	2	-
GCF_000027165.1	s__Streptococcus mitis_AR	78.6382	64	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428885.1	s__Streptococcus sp003428885	78.5569	73	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017883985.1	s__Streptococcus oricebi	78.372	61	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964575.1	s__Streptococcus suis_R	78.258	67	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018366675.1	s__Streptococcus parasanguinis_E	78.0374	51	469	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.293	95.61	95.45	0.89	0.84	13	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:26,399] [INFO] GTDB search result was written to GCF_025447695.1_ASM2544769v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:26,399] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:26,403] [INFO] DFAST_QC result json was written to GCF_025447695.1_ASM2544769v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:26,403] [INFO] DFAST_QC completed!
[2024-01-25 20:21:26,403] [INFO] Total running time: 0h0m36s