[2024-01-24 14:31:00,275] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,276] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,103] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stga5cce373-1cd3-427b-9933-2b351276ca58/GCF_003963555.1_ASM396355v1_genomic.fna.gz | prodigal -d GCF_003963555.1_ASM396355v1_genomic.fna/cds.fna -a GCF_003963555.1_ASM396355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:05,948] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:05,948] [INFO] Task started: HMMsearch
[2024-01-24 14:31:05,948] [INFO] Running command: hmmsearch --tblout GCF_003963555.1_ASM396355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/reference_markers.hmm GCF_003963555.1_ASM396355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:06,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:06,229] [INFO] Found 6/6 markers.
[2024-01-24 14:31:06,247] [INFO] Query marker FASTA was written to GCF_003963555.1_ASM396355v1_genomic.fna/markers.fasta
[2024-01-24 14:31:06,248] [INFO] Task started: Blastn
[2024-01-24 14:31:06,248] [INFO] Running command: blastn -query GCF_003963555.1_ASM396355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/reference_markers.fasta -out GCF_003963555.1_ASM396355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:08,045] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:08,048] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:08,048] [INFO] Target genome list was writen to GCF_003963555.1_ASM396355v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:08,059] [INFO] Task started: fastANI
[2024-01-24 14:31:08,059] [INFO] Running command: fastANI --query /var/lib/cwl/stga5cce373-1cd3-427b-9933-2b351276ca58/GCF_003963555.1_ASM396355v1_genomic.fna.gz --refList GCF_003963555.1_ASM396355v1_genomic.fna/target_genomes.txt --output GCF_003963555.1_ASM396355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:12,078] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:12,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:12,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:12,086] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:31:12,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:12,086] [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 anginosus subsp. anginosus	strain=FDAARGOS_1569	GCA_020735765.1	1671923	1328	type	True	96.3777	535	634	95	conclusive
Streptococcus anginosus	strain=SK52	GCA_000214555.2	1328	1328	type	True	96.3719	488	634	95	conclusive
Streptococcus anginosus	strain=DSM 20563	GCA_000373605.1	1328	1328	type	True	96.3397	535	634	95	conclusive
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	96.3393	542	634	95	conclusive
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	96.3089	548	634	95	conclusive
Streptococcus anginosus subsp. whileyi	strain=CCUG 39159	GCA_000257765.1	1272910	1328	type	True	95.8675	526	634	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	89.4798	509	634	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9999	141	634	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.5721	143	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:12,087] [INFO] DFAST Taxonomy check result was written to GCF_003963555.1_ASM396355v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:12,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:12,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:12,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/checkm_data
[2024-01-24 14:31:12,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:12,125] [INFO] Task started: CheckM
[2024-01-24 14:31:12,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003963555.1_ASM396355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003963555.1_ASM396355v1_genomic.fna/checkm_input GCF_003963555.1_ASM396355v1_genomic.fna/checkm_result
[2024-01-24 14:31:29,868] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:29,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:29,882] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:29,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:29,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003963555.1_ASM396355v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:29,882] [INFO] Task started: Blastn
[2024-01-24 14:31:29,882] [INFO] Running command: blastn -query GCF_003963555.1_ASM396355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e3600d-37ac-4550-a5eb-e8b2e3888532/dqc_reference/reference_markers_gtdb.fasta -out GCF_003963555.1_ASM396355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:30,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:30,707] [INFO] Selected 5 target genomes.
[2024-01-24 14:31:30,707] [INFO] Target genome list was writen to GCF_003963555.1_ASM396355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:30,711] [INFO] Task started: fastANI
[2024-01-24 14:31:30,711] [INFO] Running command: fastANI --query /var/lib/cwl/stga5cce373-1cd3-427b-9933-2b351276ca58/GCF_003963555.1_ASM396355v1_genomic.fna.gz --refList GCF_003963555.1_ASM396355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003963555.1_ASM396355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:33,288] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:33,292] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:31:33,293] [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_900636475.1	s__Streptococcus anginosus	96.3308	547	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.16	95.41	0.84	0.78	79	inconclusive
GCF_001697145.1	s__Streptococcus anginosus_C	95.0228	553	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.71	95.87	0.90	0.80	41	inconclusive
GCF_902167705.1	s__Streptococcus constellatus_A	91.8756	514	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900459125.1	s__Streptococcus constellatus	89.5555	500	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.83	96.57	0.88	0.81	32	-
GCF_000413475.1	s__Streptococcus intermedius	87.0008	465	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.44	98.07	0.89	0.81	45	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,294] [INFO] GTDB search result was written to GCF_003963555.1_ASM396355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:33,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:33,296] [INFO] DFAST_QC result json was written to GCF_003963555.1_ASM396355v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:33,297] [INFO] DFAST_QC completed!
[2024-01-24 14:31:33,297] [INFO] Total running time: 0h0m33s