[2024-01-25 20:07:20,603] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference
[2024-01-25 20:07:21,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,711] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg5213322a-738c-4535-9aae-9cfad528a7c5/GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna.gz | prodigal -d GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/cds.fna -a GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:25,406] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:25,407] [INFO] Task started: HMMsearch
[2024-01-25 20:07:25,407] [INFO] Running command: hmmsearch --tblout GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/reference_markers.hmm GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:25,624] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:25,625] [INFO] Found 6/6 markers.
[2024-01-25 20:07:25,644] [INFO] Query marker FASTA was written to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/markers.fasta
[2024-01-25 20:07:25,644] [INFO] Task started: Blastn
[2024-01-25 20:07:25,644] [INFO] Running command: blastn -query GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/reference_markers.fasta -out GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:26,189] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:26,191] [INFO] Selected 13 target genomes.
[2024-01-25 20:07:26,192] [INFO] Target genome list was writen to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:26,197] [INFO] Task started: fastANI
[2024-01-25 20:07:26,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg5213322a-738c-4535-9aae-9cfad528a7c5/GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna.gz --refList GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/target_genomes.txt --output GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:31,459] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:31,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:31,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:31,468] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:07:31,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:31,468] [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=ATCC 27335	GCA_000413475.1	1338	1338	type	True	100.0	640	646	95	conclusive
Streptococcus intermedius	strain=NCTC11324	GCA_900475975.1	1338	1338	type	True	99.9958	640	646	95	conclusive
Streptococcus intermedius	strain=SK54	GCA_000258445.1	1338	1338	type	True	99.9659	627	646	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=ATCC 27823	GCA_008633005.1	184246	76860	type	True	92.6837	480	646	95	below_threshold
Streptococcus constellatus subsp. pharyngis	strain=CCUG 46377	GCA_000474135.1	184250	76860	type	True	92.6184	477	646	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	92.5579	499	646	95	below_threshold
Streptococcus anginosus subsp. whileyi	strain=CCUG 39159	GCA_000257765.1	1272910	1328	type	True	88.6646	465	646	95	below_threshold
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	87.4379	475	646	95	below_threshold
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	87.434	472	646	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.1795	137	646	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.982	87	646	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.3962	81	646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:31,469] [INFO] DFAST Taxonomy check result was written to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:31,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:31,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:31,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/checkm_data
[2024-01-25 20:07:31,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:31,493] [INFO] Task started: CheckM
[2024-01-25 20:07:31,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/checkm_input GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/checkm_result
[2024-01-25 20:07:48,777] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:48,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:48,796] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:48,797] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:48,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/markers.fasta)
[2024-01-25 20:07:48,797] [INFO] Task started: Blastn
[2024-01-25 20:07:48,797] [INFO] Running command: blastn -query GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b21abcf-601e-4134-9c00-e2c5c679822d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:49,659] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:49,664] [INFO] Selected 5 target genomes.
[2024-01-25 20:07:49,664] [INFO] Target genome list was writen to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:49,671] [INFO] Task started: fastANI
[2024-01-25 20:07:49,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg5213322a-738c-4535-9aae-9cfad528a7c5/GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna.gz --refList GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:52,121] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:52,126] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:52,126] [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	100.0	639	646	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	92.6883	489	646	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	87.4575	476	646	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	87.3704	478	646	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	86.7265	461	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:52,127] [INFO] GTDB search result was written to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:52,128] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:52,132] [INFO] DFAST_QC result json was written to GCF_000413475.1_Stre_inte_ATCC_27335_V1_genomic.fna/dqc_result.json
[2024-01-25 20:07:52,132] [INFO] DFAST_QC completed!
[2024-01-25 20:07:52,132] [INFO] Total running time: 0h0m32s