[2024-01-24 11:12:40,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:40,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:40,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference
[2024-01-24 11:12:41,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,355] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e20e62c-3885-4619-a6ab-c69916ae0ef4/GCF_001921845.1_ASM192184v1_genomic.fna.gz | prodigal -d GCF_001921845.1_ASM192184v1_genomic.fna/cds.fna -a GCF_001921845.1_ASM192184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:46,585] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:46,586] [INFO] Task started: HMMsearch
[2024-01-24 11:12:46,586] [INFO] Running command: hmmsearch --tblout GCF_001921845.1_ASM192184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/reference_markers.hmm GCF_001921845.1_ASM192184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:46,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:46,857] [INFO] Found 6/6 markers.
[2024-01-24 11:12:46,880] [INFO] Query marker FASTA was written to GCF_001921845.1_ASM192184v1_genomic.fna/markers.fasta
[2024-01-24 11:12:46,881] [INFO] Task started: Blastn
[2024-01-24 11:12:46,881] [INFO] Running command: blastn -query GCF_001921845.1_ASM192184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/reference_markers.fasta -out GCF_001921845.1_ASM192184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:47,476] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:47,480] [INFO] Selected 11 target genomes.
[2024-01-24 11:12:47,480] [INFO] Target genome list was writen to GCF_001921845.1_ASM192184v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:47,484] [INFO] Task started: fastANI
[2024-01-24 11:12:47,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e20e62c-3885-4619-a6ab-c69916ae0ef4/GCF_001921845.1_ASM192184v1_genomic.fna.gz --refList GCF_001921845.1_ASM192184v1_genomic.fna/target_genomes.txt --output GCF_001921845.1_ASM192184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:53,412] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:53,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:53,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:53,428] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:53,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:53,428] [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 cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	100.0	688	688	95	conclusive
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	87.1814	527	688	95	below_threshold
Streptococcus acidominimus	strain=CCUG 27296	GCA_001921825.1	1326	1326	type	True	82.949	445	688	95	below_threshold
Streptococcus acidominimus	strain=NCTC12957	GCA_900459045.1	1326	1326	type	True	82.9048	462	688	95	below_threshold
Streptococcus marmotae	strain=HTS5	GCA_001623565.1	1825069	1825069	type	True	81.9672	422	688	95	below_threshold
Streptococcus azizii	strain=12-5202	GCA_001984715.1	1579424	1579424	type	True	81.382	406	688	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.6723	145	688	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.6027	180	688	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	77.7312	74	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:53,434] [INFO] DFAST Taxonomy check result was written to GCF_001921845.1_ASM192184v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:53,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:53,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:53,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/checkm_data
[2024-01-24 11:12:53,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:53,463] [INFO] Task started: CheckM
[2024-01-24 11:12:53,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001921845.1_ASM192184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001921845.1_ASM192184v1_genomic.fna/checkm_input GCF_001921845.1_ASM192184v1_genomic.fna/checkm_result
[2024-01-24 11:13:16,865] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:16,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:16,887] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:16,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:16,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001921845.1_ASM192184v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:16,888] [INFO] Task started: Blastn
[2024-01-24 11:13:16,888] [INFO] Running command: blastn -query GCF_001921845.1_ASM192184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22603a13-bb53-44a2-a1b5-792b1e46dd00/dqc_reference/reference_markers_gtdb.fasta -out GCF_001921845.1_ASM192184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:17,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:17,898] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:17,898] [INFO] Target genome list was writen to GCF_001921845.1_ASM192184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:17,904] [INFO] Task started: fastANI
[2024-01-24 11:13:17,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e20e62c-3885-4619-a6ab-c69916ae0ef4/GCF_001921845.1_ASM192184v1_genomic.fna.gz --refList GCF_001921845.1_ASM192184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001921845.1_ASM192184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:24,083] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:24,096] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:24,097] [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_001921845.1	s__Streptococcus cuniculi	100.0	688	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_004570575.1	s__Streptococcus cuniculi_A	91.6408	530	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_003595525.1	s__Streptococcus respiraculi	87.1505	528	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_001921825.1	s__Streptococcus acidominimus	82.949	445	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_017639855.1	s__Streptococcus sp013623465	82.2244	436	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_004569635.1	s__Streptococcus sp004569635	82.1531	455	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001623565.1	s__Streptococcus marmotae	81.9717	419	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_001708305.1	s__Streptococcus himalayensis	80.1132	225	688	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 11:13:24,099] [INFO] GTDB search result was written to GCF_001921845.1_ASM192184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:24,100] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:24,103] [INFO] DFAST_QC result json was written to GCF_001921845.1_ASM192184v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:24,103] [INFO] DFAST_QC completed!
[2024-01-24 11:13:24,103] [INFO] Total running time: 0h0m44s