[2024-01-25 19:42:05,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:05,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:05,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference
[2024-01-25 19:42:06,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:06,679] [INFO] Task started: Prodigal
[2024-01-25 19:42:06,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg966c9ecf-14f6-4481-a252-bb81a218c04f/GCF_900459225.1_48128_B02_genomic.fna.gz | prodigal -d GCF_900459225.1_48128_B02_genomic.fna/cds.fna -a GCF_900459225.1_48128_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:10,755] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:10,756] [INFO] Task started: HMMsearch
[2024-01-25 19:42:10,756] [INFO] Running command: hmmsearch --tblout GCF_900459225.1_48128_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/reference_markers.hmm GCF_900459225.1_48128_B02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:10,974] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:10,975] [INFO] Found 6/6 markers.
[2024-01-25 19:42:10,993] [INFO] Query marker FASTA was written to GCF_900459225.1_48128_B02_genomic.fna/markers.fasta
[2024-01-25 19:42:10,994] [INFO] Task started: Blastn
[2024-01-25 19:42:10,994] [INFO] Running command: blastn -query GCF_900459225.1_48128_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/reference_markers.fasta -out GCF_900459225.1_48128_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:11,555] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:11,558] [INFO] Selected 13 target genomes.
[2024-01-25 19:42:11,558] [INFO] Target genome list was writen to GCF_900459225.1_48128_B02_genomic.fna/target_genomes.txt
[2024-01-25 19:42:11,561] [INFO] Task started: fastANI
[2024-01-25 19:42:11,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg966c9ecf-14f6-4481-a252-bb81a218c04f/GCF_900459225.1_48128_B02_genomic.fna.gz --refList GCF_900459225.1_48128_B02_genomic.fna/target_genomes.txt --output GCF_900459225.1_48128_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:17,419] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:17,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:17,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:17,427] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:42:17,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:17,427] [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 dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	100.0	714	716	95	conclusive
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	99.9926	712	716	95	conclusive
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	87.4115	454	716	95	below_threshold
Streptococcus pyogenes	strain=NCTC8198	GCA_002055535.1	1314	1314	type	True	87.244	454	716	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	87.2363	452	716	95	below_threshold
Streptococcus pyogenes	strain=DSM 20565	GCA_000421785.1	1314	1314	type	True	87.2272	441	716	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	85.271	501	716	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	80.7148	191	716	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	79.6658	180	716	95	below_threshold
Streptococcus halichoeri	strain=CCUG48324	GCA_009870755.1	254785	254785	type	True	79.1139	125	716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:17,428] [INFO] DFAST Taxonomy check result was written to GCF_900459225.1_48128_B02_genomic.fna/tc_result.tsv
[2024-01-25 19:42:17,429] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:17,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:17,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/checkm_data
[2024-01-25 19:42:17,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:17,454] [INFO] Task started: CheckM
[2024-01-25 19:42:17,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459225.1_48128_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459225.1_48128_B02_genomic.fna/checkm_input GCF_900459225.1_48128_B02_genomic.fna/checkm_result
[2024-01-25 19:42:36,192] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:36,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:36,207] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:36,207] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:36,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459225.1_48128_B02_genomic.fna/markers.fasta)
[2024-01-25 19:42:36,208] [INFO] Task started: Blastn
[2024-01-25 19:42:36,208] [INFO] Running command: blastn -query GCF_900459225.1_48128_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stgd829a1ff-9997-47ae-8142-3f0ef8e99e6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459225.1_48128_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:36,980] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:36,983] [INFO] Selected 13 target genomes.
[2024-01-25 19:42:36,983] [INFO] Target genome list was writen to GCF_900459225.1_48128_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:36,986] [INFO] Task started: fastANI
[2024-01-25 19:42:36,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg966c9ecf-14f6-4481-a252-bb81a218c04f/GCF_900459225.1_48128_B02_genomic.fna.gz --refList GCF_900459225.1_48128_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900459225.1_48128_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:42,622] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:42,631] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:42,632] [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_900459225.1	s__Streptococcus dysgalactiae	100.0	713	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	conclusive
GCF_002055535.1	s__Streptococcus pyogenes	87.251	452	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_900636575.1	s__Streptococcus canis	85.2775	500	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000425025.1	s__Streptococcus castoreus	81.154	347	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188015.2	s__Streptococcus ictaluri	80.8247	308	716	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	80.6107	190	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCA_900478025.1	s__Streptococcus pasteurianus	80.2177	141	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
GCF_011421455.1	s__Streptococcus catagoni	79.6603	182	716	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	79.3184	193	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	79.2809	118	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729355.1	s__Streptococcus sp902729355	79.1675	114	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_009870755.1	s__Streptococcus halichoeri	79.1326	125	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.35	98.15	0.92	0.87	20	-
GCF_900101445.1	s__Streptococcus equinus_B	79.0916	117	716	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:42,633] [INFO] GTDB search result was written to GCF_900459225.1_48128_B02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:42,633] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:42,641] [INFO] DFAST_QC result json was written to GCF_900459225.1_48128_B02_genomic.fna/dqc_result.json
[2024-01-25 19:42:42,641] [INFO] DFAST_QC completed!
[2024-01-25 19:42:42,641] [INFO] Total running time: 0h0m37s