[2024-01-24 10:48:09,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg524a7bef-0eda-406f-90f4-081e00836058/GCF_008633005.1_ASM863300v1_genomic.fna.gz | prodigal -d GCF_008633005.1_ASM863300v1_genomic.fna/cds.fna -a GCF_008633005.1_ASM863300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:28,100] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:28,100] [INFO] Task started: HMMsearch
[2024-01-24 10:48:28,100] [INFO] Running command: hmmsearch --tblout GCF_008633005.1_ASM863300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/reference_markers.hmm GCF_008633005.1_ASM863300v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:28,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:28,356] [INFO] Found 6/6 markers.
[2024-01-24 10:48:28,377] [INFO] Query marker FASTA was written to GCF_008633005.1_ASM863300v1_genomic.fna/markers.fasta
[2024-01-24 10:48:28,378] [INFO] Task started: Blastn
[2024-01-24 10:48:28,378] [INFO] Running command: blastn -query GCF_008633005.1_ASM863300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/reference_markers.fasta -out GCF_008633005.1_ASM863300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:29,006] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:29,011] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:29,011] [INFO] Target genome list was writen to GCF_008633005.1_ASM863300v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:29,900] [INFO] Task started: fastANI
[2024-01-24 10:48:29,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg524a7bef-0eda-406f-90f4-081e00836058/GCF_008633005.1_ASM863300v1_genomic.fna.gz --refList GCF_008633005.1_ASM863300v1_genomic.fna/target_genomes.txt --output GCF_008633005.1_ASM863300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:33,463] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:33,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:33,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:33,476] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:48:33,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:33,477] [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 constellatus subsp. constellatus	strain=ATCC 27823	GCA_008633005.1	184246	76860	type	True	100.0	602	604	95	conclusive
Streptococcus constellatus	strain=NCTC11325	GCA_900459125.1	76860	76860	type	True	99.9984	604	604	95	conclusive
Streptococcus constellatus	strain=FDAARGOS_1156	GCA_016725005.1	76860	76860	type	True	99.9984	603	604	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	99.9975	604	604	95	conclusive
Streptococcus constellatus subsp. pharyngis	strain=CCUG 46377	GCA_000474135.1	184250	76860	type	True	96.9922	500	604	95	conclusive
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.1676	122	604	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.8416	148	604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,480] [INFO] DFAST Taxonomy check result was written to GCF_008633005.1_ASM863300v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:33,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:33,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:33,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/checkm_data
[2024-01-24 10:48:33,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:33,503] [INFO] Task started: CheckM
[2024-01-24 10:48:33,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008633005.1_ASM863300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008633005.1_ASM863300v1_genomic.fna/checkm_input GCF_008633005.1_ASM863300v1_genomic.fna/checkm_result
[2024-01-24 10:48:53,609] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:53,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:53,636] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:53,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:53,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008633005.1_ASM863300v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:53,637] [INFO] Task started: Blastn
[2024-01-24 10:48:53,637] [INFO] Running command: blastn -query GCF_008633005.1_ASM863300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c1e77c8-5b6f-4ec5-b179-477a4164ff5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008633005.1_ASM863300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:54,484] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:54,488] [INFO] Selected 5 target genomes.
[2024-01-24 10:48:54,488] [INFO] Target genome list was writen to GCF_008633005.1_ASM863300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:54,511] [INFO] Task started: fastANI
[2024-01-24 10:48:54,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg524a7bef-0eda-406f-90f4-081e00836058/GCF_008633005.1_ASM863300v1_genomic.fna.gz --refList GCF_008633005.1_ASM863300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008633005.1_ASM863300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:57,369] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:57,375] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:57,375] [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_900459125.1	s__Streptococcus constellatus	99.9984	604	604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.83	96.57	0.88	0.81	32	conclusive
GCF_000413475.1	s__Streptococcus intermedius	92.6311	478	604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.44	98.07	0.89	0.81	45	-
GCF_900636475.1	s__Streptococcus anginosus	89.9883	501	604	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	89.3249	517	604	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	89.1209	493	604	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 10:48:57,377] [INFO] GTDB search result was written to GCF_008633005.1_ASM863300v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:57,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:57,381] [INFO] DFAST_QC result json was written to GCF_008633005.1_ASM863300v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:57,382] [INFO] DFAST_QC completed!
[2024-01-24 10:48:57,382] [INFO] Total running time: 0h0m48s