[2024-01-24 11:43:42,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,279] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference
[2024-01-24 11:43:43,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,709] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf836b83-faf7-4a91-a2e3-04b0dfb5937f/GCF_900475595.1_44343_G01_genomic.fna.gz | prodigal -d GCF_900475595.1_44343_G01_genomic.fna/cds.fna -a GCF_900475595.1_44343_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:47,957] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:47,957] [INFO] Task started: HMMsearch
[2024-01-24 11:43:47,957] [INFO] Running command: hmmsearch --tblout GCF_900475595.1_44343_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/reference_markers.hmm GCF_900475595.1_44343_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:48,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:48,259] [INFO] Found 6/6 markers.
[2024-01-24 11:43:48,288] [INFO] Query marker FASTA was written to GCF_900475595.1_44343_G01_genomic.fna/markers.fasta
[2024-01-24 11:43:48,289] [INFO] Task started: Blastn
[2024-01-24 11:43:48,289] [INFO] Running command: blastn -query GCF_900475595.1_44343_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/reference_markers.fasta -out GCF_900475595.1_44343_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:48,903] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:48,906] [INFO] Selected 21 target genomes.
[2024-01-24 11:43:48,907] [INFO] Target genome list was writen to GCF_900475595.1_44343_G01_genomic.fna/target_genomes.txt
[2024-01-24 11:43:48,984] [INFO] Task started: fastANI
[2024-01-24 11:43:48,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf836b83-faf7-4a91-a2e3-04b0dfb5937f/GCF_900475595.1_44343_G01_genomic.fna.gz --refList GCF_900475595.1_44343_G01_genomic.fna/target_genomes.txt --output GCF_900475595.1_44343_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:58,010] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:58,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:58,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:58,026] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:58,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:58,027] [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 uberis	strain=NCTC3858	GCA_900475595.1	1349	1349	type	True	100.0	656	658	95	conclusive
Streptococcus bovimastitidis	strain=NZ1587	GCA_001885095.1	1856638	1856638	type	True	81.0582	324	658	95	below_threshold
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	80.6789	312	658	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	80.4551	255	658	95	below_threshold
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	80.3239	186	658	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.1872	62	658	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	80.1101	185	658	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	79.9796	231	658	95	below_threshold
Streptococcus parauberis	strain=NCFD 2020	GCA_000187935.2	1348	1348	type	True	79.6963	281	658	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	79.6283	133	658	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	79.6206	131	658	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	79.3364	197	658	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.2015	88	658	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	78.8968	218	658	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.7839	130	658	95	below_threshold
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	78.6562	87	658	95	below_threshold
Streptococcus thoraltensis	strain=DSM 12221	GCA_000380145.1	55085	55085	type	True	78.6104	119	658	95	below_threshold
Streptococcus halichoeri	strain=CCUG48324	GCA_009870755.1	254785	254785	type	True	78.5804	114	658	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.5466	116	658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:58,028] [INFO] DFAST Taxonomy check result was written to GCF_900475595.1_44343_G01_genomic.fna/tc_result.tsv
[2024-01-24 11:43:58,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:58,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:58,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/checkm_data
[2024-01-24 11:43:58,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:58,052] [INFO] Task started: CheckM
[2024-01-24 11:43:58,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475595.1_44343_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475595.1_44343_G01_genomic.fna/checkm_input GCF_900475595.1_44343_G01_genomic.fna/checkm_result
[2024-01-24 11:44:19,023] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:19,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:19,065] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:19,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:19,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475595.1_44343_G01_genomic.fna/markers.fasta)
[2024-01-24 11:44:19,066] [INFO] Task started: Blastn
[2024-01-24 11:44:19,066] [INFO] Running command: blastn -query GCF_900475595.1_44343_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb05410d-8a79-4a8a-89d5-3a13a9aaba93/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475595.1_44343_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:19,940] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:19,945] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:19,945] [INFO] Target genome list was writen to GCF_900475595.1_44343_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:19,958] [INFO] Task started: fastANI
[2024-01-24 11:44:19,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf836b83-faf7-4a91-a2e3-04b0dfb5937f/GCF_900475595.1_44343_G01_genomic.fna.gz --refList GCF_900475595.1_44343_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475595.1_44343_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:26,051] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:26,068] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:26,069] [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_900475595.1	s__Streptococcus uberis	100.0	656	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.97	98.11	0.91	0.87	68	conclusive
GCF_001885095.1	s__Streptococcus bovimastitidis	81.0582	324	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887775.1	s__Streptococcus penaeicida	80.6665	313	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475415.1	s__Streptococcus porcinus	80.4738	256	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_901542335.1	s__Streptococcus porcinus_A	80.3829	254	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_900459225.1	s__Streptococcus dysgalactiae	80.2862	190	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_900636575.1	s__Streptococcus canis	79.9714	162	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000187935.1	s__Streptococcus parauberis	79.6398	280	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_011421455.1	s__Streptococcus catagoni	79.4205	195	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003674745.1	s__Streptococcus iniae	79.2696	237	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_000785785.1	s__Streptococcus uberis_A	79.1144	215	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010604095.1	s__Streptococcus sp000187445	79.048	88	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000380005.1	s__Streptococcus didelphis	78.8968	218	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	78.6086	120	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_009870755.1	s__Streptococcus halichoeri	78.5804	114	658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.35	98.15	0.92	0.87	20	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,070] [INFO] GTDB search result was written to GCF_900475595.1_44343_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:26,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:26,079] [INFO] DFAST_QC result json was written to GCF_900475595.1_44343_G01_genomic.fna/dqc_result.json
[2024-01-24 11:44:26,079] [INFO] DFAST_QC completed!
[2024-01-24 11:44:26,079] [INFO] Total running time: 0h0m44s