[2024-01-24 14:19:14,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:14,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:14,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference
[2024-01-24 14:19:16,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,026] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg21d3300b-15bc-42e1-b789-a083f5a9f6fc/GCF_019972895.1_ASM1997289v1_genomic.fna.gz | prodigal -d GCF_019972895.1_ASM1997289v1_genomic.fna/cds.fna -a GCF_019972895.1_ASM1997289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:20,908] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:20,909] [INFO] Task started: HMMsearch
[2024-01-24 14:19:20,909] [INFO] Running command: hmmsearch --tblout GCF_019972895.1_ASM1997289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/reference_markers.hmm GCF_019972895.1_ASM1997289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:21,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:21,102] [INFO] Found 6/6 markers.
[2024-01-24 14:19:21,123] [INFO] Query marker FASTA was written to GCF_019972895.1_ASM1997289v1_genomic.fna/markers.fasta
[2024-01-24 14:19:21,124] [INFO] Task started: Blastn
[2024-01-24 14:19:21,124] [INFO] Running command: blastn -query GCF_019972895.1_ASM1997289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/reference_markers.fasta -out GCF_019972895.1_ASM1997289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:21,693] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:21,696] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:21,696] [INFO] Target genome list was writen to GCF_019972895.1_ASM1997289v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:21,700] [INFO] Task started: fastANI
[2024-01-24 14:19:21,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d3300b-15bc-42e1-b789-a083f5a9f6fc/GCF_019972895.1_ASM1997289v1_genomic.fna.gz --refList GCF_019972895.1_ASM1997289v1_genomic.fna/target_genomes.txt --output GCF_019972895.1_ASM1997289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:26,131] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:26,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:26,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:26,141] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:19:26,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:26,141] [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=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	100.0	707	708	95	conclusive
Streptococcus salivarius	strain=NCTC8618	GCA_900636435.1	1304	1304	suspected-type	True	99.9991	707	708	95	conclusive
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	99.9883	706	708	95	conclusive
Streptococcus salivarius	strain=ATCC 7073	GCA_900143035.1	1304	1304	suspected-type	True	99.9638	707	708	95	conclusive
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	92.0183	515	708	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	89.0969	474	708	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	80.0161	177	708	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.438	89	708	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.9284	70	708	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.3079	74	708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:26,143] [INFO] DFAST Taxonomy check result was written to GCF_019972895.1_ASM1997289v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:26,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:26,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:26,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/checkm_data
[2024-01-24 14:19:26,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:26,171] [INFO] Task started: CheckM
[2024-01-24 14:19:26,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019972895.1_ASM1997289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019972895.1_ASM1997289v1_genomic.fna/checkm_input GCF_019972895.1_ASM1997289v1_genomic.fna/checkm_result
[2024-01-24 14:19:48,281] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:48,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,300] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:48,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:48,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019972895.1_ASM1997289v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:48,302] [INFO] Task started: Blastn
[2024-01-24 14:19:48,302] [INFO] Running command: blastn -query GCF_019972895.1_ASM1997289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e76b830-1247-4ed2-bc07-ce11d9ed681e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019972895.1_ASM1997289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:49,210] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:49,213] [INFO] Selected 6 target genomes.
[2024-01-24 14:19:49,213] [INFO] Target genome list was writen to GCF_019972895.1_ASM1997289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:49,231] [INFO] Task started: fastANI
[2024-01-24 14:19:49,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg21d3300b-15bc-42e1-b789-a083f5a9f6fc/GCF_019972895.1_ASM1997289v1_genomic.fna.gz --refList GCF_019972895.1_ASM1997289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019972895.1_ASM1997289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:52,542] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:52,549] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:52,549] [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	99.9883	706	708	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	94.8777	639	708	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	93.3694	428	708	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	92.0183	515	708	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	89.7971	574	708	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	88.9732	501	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:52,550] [INFO] GTDB search result was written to GCF_019972895.1_ASM1997289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:52,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:52,553] [INFO] DFAST_QC result json was written to GCF_019972895.1_ASM1997289v1_genomic.fna/dqc_result.json
[2024-01-24 14:19:52,554] [INFO] DFAST_QC completed!
[2024-01-24 14:19:52,554] [INFO] Total running time: 0h0m38s