[2024-01-24 12:51:05,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,258] [INFO] DQC Reference Directory: /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference
[2024-01-24 12:51:06,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,463] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,463] [INFO] Running command: gunzip -c /var/lib/cwl/stgeef5e0ad-8dd3-44e9-ba25-4ab3a85be6f6/GCF_900475975.1_46931_F01_genomic.fna.gz | prodigal -d GCF_900475975.1_46931_F01_genomic.fna/cds.fna -a GCF_900475975.1_46931_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:10,723] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:10,723] [INFO] Task started: HMMsearch
[2024-01-24 12:51:10,724] [INFO] Running command: hmmsearch --tblout GCF_900475975.1_46931_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/reference_markers.hmm GCF_900475975.1_46931_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:10,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:10,976] [INFO] Found 6/6 markers.
[2024-01-24 12:51:11,004] [INFO] Query marker FASTA was written to GCF_900475975.1_46931_F01_genomic.fna/markers.fasta
[2024-01-24 12:51:11,004] [INFO] Task started: Blastn
[2024-01-24 12:51:11,004] [INFO] Running command: blastn -query GCF_900475975.1_46931_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/reference_markers.fasta -out GCF_900475975.1_46931_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:11,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:11,587] [INFO] Selected 13 target genomes.
[2024-01-24 12:51:11,588] [INFO] Target genome list was writen to GCF_900475975.1_46931_F01_genomic.fna/target_genomes.txt
[2024-01-24 12:51:11,600] [INFO] Task started: fastANI
[2024-01-24 12:51:11,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef5e0ad-8dd3-44e9-ba25-4ab3a85be6f6/GCF_900475975.1_46931_F01_genomic.fna.gz --refList GCF_900475975.1_46931_F01_genomic.fna/target_genomes.txt --output GCF_900475975.1_46931_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:16,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:16,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:16,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:16,762] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:51:16,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:16,763] [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 intermedius	strain=NCTC11324	GCA_900475975.1	1338	1338	type	True	100.0	642	644	95	conclusive
Streptococcus intermedius	strain=ATCC 27335	GCA_000413475.1	1338	1338	type	True	99.9818	638	644	95	conclusive
Streptococcus intermedius	strain=SK54	GCA_000258445.1	1338	1338	type	True	99.9583	629	644	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=ATCC 27823	GCA_008633005.1	184246	76860	type	True	92.6211	483	644	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	92.5833	495	644	95	below_threshold
Streptococcus constellatus subsp. pharyngis	strain=CCUG 46377	GCA_000474135.1	184250	76860	type	True	92.35	486	644	95	below_threshold
Streptococcus anginosus subsp. whileyi	strain=CCUG 39159	GCA_000257765.1	1272910	1328	type	True	88.3913	490	644	95	below_threshold
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	87.4117	477	644	95	below_threshold
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	87.283	475	644	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.4344	87	644	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.1922	131	644	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.5444	82	644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:16,765] [INFO] DFAST Taxonomy check result was written to GCF_900475975.1_46931_F01_genomic.fna/tc_result.tsv
[2024-01-24 12:51:16,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:16,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:16,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/checkm_data
[2024-01-24 12:51:16,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:16,790] [INFO] Task started: CheckM
[2024-01-24 12:51:16,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475975.1_46931_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475975.1_46931_F01_genomic.fna/checkm_input GCF_900475975.1_46931_F01_genomic.fna/checkm_result
[2024-01-24 12:51:36,667] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:36,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:36,685] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:36,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:36,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475975.1_46931_F01_genomic.fna/markers.fasta)
[2024-01-24 12:51:36,686] [INFO] Task started: Blastn
[2024-01-24 12:51:36,686] [INFO] Running command: blastn -query GCF_900475975.1_46931_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stga8bfa8fc-fdf2-4b4a-b9b2-13298a005417/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475975.1_46931_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:37,484] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:37,488] [INFO] Selected 5 target genomes.
[2024-01-24 12:51:37,488] [INFO] Target genome list was writen to GCF_900475975.1_46931_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:51:37,498] [INFO] Task started: fastANI
[2024-01-24 12:51:37,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef5e0ad-8dd3-44e9-ba25-4ab3a85be6f6/GCF_900475975.1_46931_F01_genomic.fna.gz --refList GCF_900475975.1_46931_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475975.1_46931_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:40,016] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:40,025] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:40,025] [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_000413475.1	s__Streptococcus intermedius	99.9818	639	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.44	98.07	0.89	0.81	45	conclusive
GCF_900459125.1	s__Streptococcus constellatus	92.532	492	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.83	96.57	0.88	0.81	32	-
GCF_900636475.1	s__Streptococcus anginosus	87.4048	477	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.16	95.41	0.84	0.78	79	-
GCF_001697145.1	s__Streptococcus anginosus_C	87.195	487	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.71	95.87	0.90	0.80	41	-
GCF_902167705.1	s__Streptococcus constellatus_A	86.6274	464	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:51:40,027] [INFO] GTDB search result was written to GCF_900475975.1_46931_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:40,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:40,030] [INFO] DFAST_QC result json was written to GCF_900475975.1_46931_F01_genomic.fna/dqc_result.json
[2024-01-24 12:51:40,030] [INFO] DFAST_QC completed!
[2024-01-24 12:51:40,030] [INFO] Total running time: 0h0m35s