[2024-01-24 12:31:18,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:18,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:18,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference
[2024-01-24 12:31:19,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:19,270] [INFO] Task started: Prodigal
[2024-01-24 12:31:19,270] [INFO] Running command: gunzip -c /var/lib/cwl/stgad4ceba8-1015-46fa-974d-3cf1e089ef48/GCF_000258445.1_SintermediusSK54v1.0_genomic.fna.gz | prodigal -d GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/cds.fna -a GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:22,861] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:22,861] [INFO] Task started: HMMsearch
[2024-01-24 12:31:22,861] [INFO] Running command: hmmsearch --tblout GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/reference_markers.hmm GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:23,065] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:23,070] [INFO] Found 6/6 markers.
[2024-01-24 12:31:23,091] [INFO] Query marker FASTA was written to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/markers.fasta
[2024-01-24 12:31:23,091] [INFO] Task started: Blastn
[2024-01-24 12:31:23,092] [INFO] Running command: blastn -query GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/reference_markers.fasta -out GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,637] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,640] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:23,640] [INFO] Target genome list was writen to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:31:23,644] [INFO] Task started: fastANI
[2024-01-24 12:31:23,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4ceba8-1015-46fa-974d-3cf1e089ef48/GCF_000258445.1_SintermediusSK54v1.0_genomic.fna.gz --refList GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/target_genomes.txt --output GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:28,873] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:28,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:28,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:28,882] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:28,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:28,882] [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=SK54	GCA_000258445.1	1338	1338	type	True	100.0	628	628	95	conclusive
Streptococcus intermedius	strain=NCTC11324	GCA_900475975.1	1338	1338	type	True	99.9971	628	628	95	conclusive
Streptococcus intermedius	strain=ATCC 27335	GCA_000413475.1	1338	1338	type	True	99.996	627	628	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=ATCC 27823	GCA_008633005.1	184246	76860	type	True	92.7248	467	628	95	below_threshold
Streptococcus constellatus subsp. pharyngis	strain=CCUG 46377	GCA_000474135.1	184250	76860	type	True	92.7137	472	628	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	92.5282	486	628	95	below_threshold
Streptococcus anginosus subsp. whileyi	strain=CCUG 39159	GCA_000257765.1	1272910	1328	type	True	88.5728	476	628	95	below_threshold
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	87.464	466	628	95	below_threshold
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	87.4175	469	628	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.9337	129	628	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.2345	77	628	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.6163	75	628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:28,883] [INFO] DFAST Taxonomy check result was written to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:31:28,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:28,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:28,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/checkm_data
[2024-01-24 12:31:28,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:28,910] [INFO] Task started: CheckM
[2024-01-24 12:31:28,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/checkm_input GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/checkm_result
[2024-01-24 12:31:45,567] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:45,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,584] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:45,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:45,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/markers.fasta)
[2024-01-24 12:31:45,585] [INFO] Task started: Blastn
[2024-01-24 12:31:45,585] [INFO] Running command: blastn -query GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg5257dd39-3ed7-4070-8de8-2e7e8793ad21/dqc_reference/reference_markers_gtdb.fasta -out GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,334] [INFO] Selected 5 target genomes.
[2024-01-24 12:31:46,334] [INFO] Target genome list was writen to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:46,337] [INFO] Task started: fastANI
[2024-01-24 12:31:46,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4ceba8-1015-46fa-974d-3cf1e089ef48/GCF_000258445.1_SintermediusSK54v1.0_genomic.fna.gz --refList GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:48,644] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,648] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:48,649] [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	99.996	627	628	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	92.5091	489	628	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	87.4175	469	628	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	87.1653	480	628	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	86.6144	457	628	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 12:31:48,650] [INFO] GTDB search result was written to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:48,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:48,699] [INFO] DFAST_QC result json was written to GCF_000258445.1_SintermediusSK54v1.0_genomic.fna/dqc_result.json
[2024-01-24 12:31:48,699] [INFO] DFAST_QC completed!
[2024-01-24 12:31:48,699] [INFO] Total running time: 0h0m31s