[2024-01-24 11:12:48,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference
[2024-01-24 11:12:49,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,926] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgdecdcefe-d91b-4b02-a029-12ca6410aa64/GCF_900475015.1_41975_E01_genomic.fna.gz | prodigal -d GCF_900475015.1_41975_E01_genomic.fna/cds.fna -a GCF_900475015.1_41975_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:54,755] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:54,755] [INFO] Task started: HMMsearch
[2024-01-24 11:12:54,756] [INFO] Running command: hmmsearch --tblout GCF_900475015.1_41975_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/reference_markers.hmm GCF_900475015.1_41975_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:55,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:55,015] [INFO] Found 6/6 markers.
[2024-01-24 11:12:55,038] [INFO] Query marker FASTA was written to GCF_900475015.1_41975_E01_genomic.fna/markers.fasta
[2024-01-24 11:12:55,039] [INFO] Task started: Blastn
[2024-01-24 11:12:55,039] [INFO] Running command: blastn -query GCF_900475015.1_41975_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/reference_markers.fasta -out GCF_900475015.1_41975_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:55,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:55,629] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:55,629] [INFO] Target genome list was writen to GCF_900475015.1_41975_E01_genomic.fna/target_genomes.txt
[2024-01-24 11:12:55,828] [INFO] Task started: fastANI
[2024-01-24 11:12:55,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgdecdcefe-d91b-4b02-a029-12ca6410aa64/GCF_900475015.1_41975_E01_genomic.fna.gz --refList GCF_900475015.1_41975_E01_genomic.fna/target_genomes.txt --output GCF_900475015.1_41975_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:01,280] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:01,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:01,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:01,296] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:13:01,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:01,296] [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 gordonii	strain=NCTC7865	GCA_900475015.1	1302	1302	suspected-type	True	100.0	727	729	95	conclusive
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	99.9983	727	729	95	conclusive
Streptococcus gordonii	strain=CCUG 33482	GCA_001553855.1	1302	1302	suspected-type	True	99.9873	709	729	95	conclusive
Streptococcus gordonii	strain=ATCC 10558	GCA_001469295.1	1302	1302	suspected-type	True	99.9724	713	729	95	conclusive
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	86.4999	432	729	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	84.4801	361	729	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000187855.1	45634	45634	type	True	83.9971	346	729	95	below_threshold
Streptococcus sinensis	strain=HKU4	GCA_000767835.1	176090	176090	type	True	83.4795	316	729	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	81.6729	198	729	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	81.5813	185	729	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.6306	180	729	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	80.4594	189	729	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.7477	104	729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:01,298] [INFO] DFAST Taxonomy check result was written to GCF_900475015.1_41975_E01_genomic.fna/tc_result.tsv
[2024-01-24 11:13:01,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:01,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:01,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/checkm_data
[2024-01-24 11:13:01,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:01,322] [INFO] Task started: CheckM
[2024-01-24 11:13:01,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475015.1_41975_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475015.1_41975_E01_genomic.fna/checkm_input GCF_900475015.1_41975_E01_genomic.fna/checkm_result
[2024-01-24 11:13:25,342] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:25,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:25,362] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:25,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:25,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475015.1_41975_E01_genomic.fna/markers.fasta)
[2024-01-24 11:13:25,363] [INFO] Task started: Blastn
[2024-01-24 11:13:25,364] [INFO] Running command: blastn -query GCF_900475015.1_41975_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2688838-75bc-4657-874a-2d8e4581325e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475015.1_41975_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:26,159] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:26,162] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:26,162] [INFO] Target genome list was writen to GCF_900475015.1_41975_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:26,184] [INFO] Task started: fastANI
[2024-01-24 11:13:26,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgdecdcefe-d91b-4b02-a029-12ca6410aa64/GCF_900475015.1_41975_E01_genomic.fna.gz --refList GCF_900475015.1_41975_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475015.1_41975_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:33,756] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:33,781] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:33,782] [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_001553855.1	s__Streptococcus gordonii	99.9873	709	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.12	95.48	0.92	0.82	64	conclusive
GCA_001578795.1	s__Streptococcus gordonii_A	94.783	640	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212815.1	s__Streptococcus sanguinis_C	86.6007	429	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.73	95.65	0.92	0.92	3	-
GCF_013343115.1	s__Streptococcus sanguinis_H	86.4976	445	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_003943655.1	s__Streptococcus sanguinis_F	86.4105	424	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	96.90	0.96	0.95	3	-
GCF_001078705.1	s__Streptococcus sanguinis_D	86.1554	425	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212855.1	s__Streptococcus sanguinis_A	86.0578	412	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372115.1	s__Streptococcus sp905372115	86.0164	402	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635155.1	s__Streptococcus sanguinis_G	85.9132	441	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.44	97.44	0.92	0.92	2	-
GCA_013378335.1	s__Streptococcus sanguinis_I	85.7242	442	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.17	96.17	0.87	0.87	2	-
GCF_000220065.1	s__Streptococcus sp000220065	85.6078	431	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.21	96.21	0.86	0.86	2	-
GCF_003943815.1	s__Streptococcus cristatus_F	84.2096	338	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943505.1	s__Streptococcus cristatus_E	84.1527	337	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222765.1	s__Streptococcus cristatus	84.0611	366	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.39	95.04	0.92	0.87	17	-
GCF_902460355.1	s__Streptococcus sp902460355	84.0086	355	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369405.1	s__Streptococcus cristatus_G	83.8633	338	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385925.1	s__Streptococcus cristatus_B	83.609	356	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.95	99.95	1.00	0.99	3	-
GCF_000767835.1	s__Streptococcus sinensis	83.4788	316	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.90	95.29	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:33,783] [INFO] GTDB search result was written to GCF_900475015.1_41975_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:33,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:33,788] [INFO] DFAST_QC result json was written to GCF_900475015.1_41975_E01_genomic.fna/dqc_result.json
[2024-01-24 11:13:33,788] [INFO] DFAST_QC completed!
[2024-01-24 11:13:33,788] [INFO] Total running time: 0h0m45s