[2023-06-19 06:19:20,549] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:19:20,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:19:20,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference
[2023-06-19 06:19:24,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:19:24,189] [INFO] Task started: Prodigal
[2023-06-19 06:19:24,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e3a57a8-99f2-485d-80b9-ab1f4c8426f3/GCA_018381705.1_ASM1838170v1_genomic.fna.gz | prodigal -d GCA_018381705.1_ASM1838170v1_genomic.fna/cds.fna -a GCA_018381705.1_ASM1838170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:19:28,614] [INFO] Task succeeded: Prodigal
[2023-06-19 06:19:28,614] [INFO] Task started: HMMsearch
[2023-06-19 06:19:28,614] [INFO] Running command: hmmsearch --tblout GCA_018381705.1_ASM1838170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/reference_markers.hmm GCA_018381705.1_ASM1838170v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:19:28,901] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:19:28,903] [INFO] Found 6/6 markers.
[2023-06-19 06:19:28,928] [INFO] Query marker FASTA was written to GCA_018381705.1_ASM1838170v1_genomic.fna/markers.fasta
[2023-06-19 06:19:28,929] [INFO] Task started: Blastn
[2023-06-19 06:19:28,929] [INFO] Running command: blastn -query GCA_018381705.1_ASM1838170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/reference_markers.fasta -out GCA_018381705.1_ASM1838170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:29,575] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:29,580] [INFO] Selected 11 target genomes.
[2023-06-19 06:19:29,581] [INFO] Target genome list was writen to GCA_018381705.1_ASM1838170v1_genomic.fna/target_genomes.txt
[2023-06-19 06:19:29,583] [INFO] Task started: fastANI
[2023-06-19 06:19:29,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3a57a8-99f2-485d-80b9-ab1f4c8426f3/GCA_018381705.1_ASM1838170v1_genomic.fna.gz --refList GCA_018381705.1_ASM1838170v1_genomic.fna/target_genomes.txt --output GCA_018381705.1_ASM1838170v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:19:34,211] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:34,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:19:34,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:19:34,233] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-19 06:19:34,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 06:19:34,233] [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 salivarius	strain=NCTC8618	GCA_900636435.1	1304	1304	suspected-type	True	95.6519	513	623	95	conclusive
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	95.6491	509	623	95	conclusive
Streptococcus salivarius	strain=ATCC 7073	GCA_900143035.1	1304	1304	suspected-type	True	95.6459	510	623	95	conclusive
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	95.6435	517	623	95	conclusive
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	91.69	456	623	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	88.9042	432	623	95	below_threshold
Streptococcus hyovaginalis	strain=DSM 12219	GCA_000420785.1	149015	149015	type	True	79.226	90	623	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.0233	117	623	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.8342	57	623	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.7525	84	623	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.1107	58	623	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:19:34,237] [INFO] DFAST Taxonomy check result was written to GCA_018381705.1_ASM1838170v1_genomic.fna/tc_result.tsv
[2023-06-19 06:19:34,237] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:19:34,238] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:19:34,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/checkm_data
[2023-06-19 06:19:34,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:19:34,269] [INFO] Task started: CheckM
[2023-06-19 06:19:34,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381705.1_ASM1838170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381705.1_ASM1838170v1_genomic.fna/checkm_input GCA_018381705.1_ASM1838170v1_genomic.fna/checkm_result
[2023-06-19 06:19:55,184] [INFO] Task succeeded: CheckM
[2023-06-19 06:19:55,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:19:55,237] [INFO] ===== Completeness check finished =====
[2023-06-19 06:19:55,237] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:19:55,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381705.1_ASM1838170v1_genomic.fna/markers.fasta)
[2023-06-19 06:19:55,238] [INFO] Task started: Blastn
[2023-06-19 06:19:55,238] [INFO] Running command: blastn -query GCA_018381705.1_ASM1838170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c6ffce7-8ab6-4f96-ada5-c30e467b0491/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381705.1_ASM1838170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:19:56,271] [INFO] Task succeeded: Blastn
[2023-06-19 06:19:56,277] [INFO] Selected 6 target genomes.
[2023-06-19 06:19:56,277] [INFO] Target genome list was writen to GCA_018381705.1_ASM1838170v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:19:56,278] [INFO] Task started: fastANI
[2023-06-19 06:19:56,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3a57a8-99f2-485d-80b9-ab1f4c8426f3/GCA_018381705.1_ASM1838170v1_genomic.fna.gz --refList GCA_018381705.1_ASM1838170v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381705.1_ASM1838170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:19:59,385] [INFO] Task succeeded: fastANI
[2023-06-19 06:19:59,399] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:19:59,399] [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_000785515.1	s__Streptococcus salivarius	95.6435	517	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	conclusive
GCF_009738225.1	s__Streptococcus sp001556435	94.1624	559	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCA_003521145.1	s__Streptococcus sp003521145	93.3053	381	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188295.1	s__Streptococcus vestibularis	91.7132	455	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.03	95.83	0.91	0.87	14	-
GCF_010604095.1	s__Streptococcus sp000187445	89.5125	479	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_010120595.1	s__Streptococcus thermophilus	88.7748	447	623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	-
--------------------------------------------------------------------------------
[2023-06-19 06:19:59,401] [INFO] GTDB search result was written to GCA_018381705.1_ASM1838170v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:19:59,402] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:19:59,406] [INFO] DFAST_QC result json was written to GCA_018381705.1_ASM1838170v1_genomic.fna/dqc_result.json
[2023-06-19 06:19:59,406] [INFO] DFAST_QC completed!
[2023-06-19 06:19:59,406] [INFO] Total running time: 0h0m39s