[2024-01-24 14:06:07,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference
[2024-01-24 14:06:08,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,633] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg65fcbc0a-440b-4a18-945c-8cbffd4d6f7b/GCF_003595525.1_ASM359552v1_genomic.fna.gz | prodigal -d GCF_003595525.1_ASM359552v1_genomic.fna/cds.fna -a GCF_003595525.1_ASM359552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:13,706] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:13,706] [INFO] Task started: HMMsearch
[2024-01-24 14:06:13,706] [INFO] Running command: hmmsearch --tblout GCF_003595525.1_ASM359552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/reference_markers.hmm GCF_003595525.1_ASM359552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:13,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:13,990] [INFO] Found 6/6 markers.
[2024-01-24 14:06:14,014] [INFO] Query marker FASTA was written to GCF_003595525.1_ASM359552v1_genomic.fna/markers.fasta
[2024-01-24 14:06:14,014] [INFO] Task started: Blastn
[2024-01-24 14:06:14,015] [INFO] Running command: blastn -query GCF_003595525.1_ASM359552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/reference_markers.fasta -out GCF_003595525.1_ASM359552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:14,723] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:14,727] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:14,728] [INFO] Target genome list was writen to GCF_003595525.1_ASM359552v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:14,740] [INFO] Task started: fastANI
[2024-01-24 14:06:14,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fcbc0a-440b-4a18-945c-8cbffd4d6f7b/GCF_003595525.1_ASM359552v1_genomic.fna.gz --refList GCF_003595525.1_ASM359552v1_genomic.fna/target_genomes.txt --output GCF_003595525.1_ASM359552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:21,357] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:21,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:21,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:21,369] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:21,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:21,370] [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 respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	100.0	682	688	95	conclusive
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	87.0881	533	688	95	below_threshold
Streptococcus marmotae	strain=HTS5	GCA_001623565.1	1825069	1825069	type	True	85.9081	452	688	95	below_threshold
Streptococcus himalayensis	strain=HTS2	GCA_001708305.1	1888195	1888195	type	True	83.7701	239	688	95	below_threshold
Streptococcus himalayensis	strain=CGMCC 1.15533	GCA_014643475.1	1888195	1888195	type	True	83.4748	227	688	95	below_threshold
Streptococcus acidominimus	strain=NCTC12957	GCA_900459045.1	1326	1326	type	True	82.5495	454	688	95	below_threshold
Streptococcus acidominimus	strain=CCUG 27296	GCA_001921825.1	1326	1326	type	True	82.356	428	688	95	below_threshold
Streptococcus azizii	strain=12-5202	GCA_001984715.1	1579424	1579424	type	True	81.2354	379	688	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	80.6526	99	688	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	80.1246	79	688	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.1735	147	688	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9444	124	688	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.6853	101	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:21,373] [INFO] DFAST Taxonomy check result was written to GCF_003595525.1_ASM359552v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:21,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:21,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:21,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/checkm_data
[2024-01-24 14:06:21,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:21,404] [INFO] Task started: CheckM
[2024-01-24 14:06:21,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003595525.1_ASM359552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003595525.1_ASM359552v1_genomic.fna/checkm_input GCF_003595525.1_ASM359552v1_genomic.fna/checkm_result
[2024-01-24 14:06:44,504] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:44,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,528] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:44,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:44,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003595525.1_ASM359552v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:44,530] [INFO] Task started: Blastn
[2024-01-24 14:06:44,530] [INFO] Running command: blastn -query GCF_003595525.1_ASM359552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg190575b0-36e5-4a0b-9dea-bc2374f56388/dqc_reference/reference_markers_gtdb.fasta -out GCF_003595525.1_ASM359552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,401] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,405] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:45,406] [INFO] Target genome list was writen to GCF_003595525.1_ASM359552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:45,413] [INFO] Task started: fastANI
[2024-01-24 14:06:45,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fcbc0a-440b-4a18-945c-8cbffd4d6f7b/GCF_003595525.1_ASM359552v1_genomic.fna.gz --refList GCF_003595525.1_ASM359552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003595525.1_ASM359552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:50,984] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:50,992] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:50,993] [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_003595525.1	s__Streptococcus respiraculi	100.0	685	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001921845.1	s__Streptococcus cuniculi	87.0931	532	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639855.1	s__Streptococcus sp013623465	86.1915	470	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.93	0.99	0.98	7	-
GCF_001623565.1	s__Streptococcus marmotae	85.9036	452	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570575.1	s__Streptococcus cuniculi_A	85.7341	480	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001708305.1	s__Streptococcus himalayensis	83.8504	234	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001921825.1	s__Streptococcus acidominimus	82.3374	429	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.52	97.98	0.90	0.85	5	-
GCF_004569635.1	s__Streptococcus sp004569635	81.977	436	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:51,192] [INFO] GTDB search result was written to GCF_003595525.1_ASM359552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:51,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:51,197] [INFO] DFAST_QC result json was written to GCF_003595525.1_ASM359552v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:51,197] [INFO] DFAST_QC completed!
[2024-01-24 14:06:51,197] [INFO] Total running time: 0h0m44s