[2024-01-24 12:06:24,804] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,806] [INFO] DQC Reference Directory: /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference
[2024-01-24 12:06:26,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,140] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,140] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2b7bfc8-93d3-4fc2-a44a-509b819bd157/GCF_016481285.1_ASM1648128v1_genomic.fna.gz | prodigal -d GCF_016481285.1_ASM1648128v1_genomic.fna/cds.fna -a GCF_016481285.1_ASM1648128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,233] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,234] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,234] [INFO] Running command: hmmsearch --tblout GCF_016481285.1_ASM1648128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/reference_markers.hmm GCF_016481285.1_ASM1648128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:29,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:29,466] [INFO] Found 6/6 markers.
[2024-01-24 12:06:29,489] [INFO] Query marker FASTA was written to GCF_016481285.1_ASM1648128v1_genomic.fna/markers.fasta
[2024-01-24 12:06:29,489] [INFO] Task started: Blastn
[2024-01-24 12:06:29,489] [INFO] Running command: blastn -query GCF_016481285.1_ASM1648128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/reference_markers.fasta -out GCF_016481285.1_ASM1648128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,123] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,128] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:30,129] [INFO] Target genome list was writen to GCF_016481285.1_ASM1648128v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,139] [INFO] Task started: fastANI
[2024-01-24 12:06:30,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2b7bfc8-93d3-4fc2-a44a-509b819bd157/GCF_016481285.1_ASM1648128v1_genomic.fna.gz --refList GCF_016481285.1_ASM1648128v1_genomic.fna/target_genomes.txt --output GCF_016481285.1_ASM1648128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,308] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:37,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:37,308] [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 zalophi	strain=CSL7508	GCA_016481285.1	640031	640031	type	True	100.0	518	518	95	conclusive
Streptococcus pacificus	strain=CSL7591	GCA_016481305.1	2740577	2740577	type	True	87.9121	447	518	95	below_threshold
Streptococcus marimammalium	strain=DSM 18627	GCA_000380045.1	269666	269666	type	True	87.4657	409	518	95	below_threshold
Streptococcus hyointestinalis	strain=NCTC12224	GCA_900459405.1	1337	1337	type	True	78.5572	59	518	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	78.5024	85	518	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	78.4549	87	518	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.3545	59	518	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.3299	85	518	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	78.2908	88	518	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.182	102	518	95	below_threshold
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	78.0368	87	518	95	below_threshold
Streptococcus urinalis	strain=NCTC13766	GCA_900636885.1	149016	149016	type	True	78.0206	105	518	95	below_threshold
Streptococcus urinalis	strain=2285-97	GCA_000188055.3	149016	149016	type	True	77.9774	106	518	95	below_threshold
Streptococcus thoraltensis	strain=DSM 12221	GCA_000380145.1	55085	55085	type	True	77.826	88	518	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	77.767	66	518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,312] [INFO] DFAST Taxonomy check result was written to GCF_016481285.1_ASM1648128v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/checkm_data
[2024-01-24 12:06:37,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:37,333] [INFO] Task started: CheckM
[2024-01-24 12:06:37,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016481285.1_ASM1648128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016481285.1_ASM1648128v1_genomic.fna/checkm_input GCF_016481285.1_ASM1648128v1_genomic.fna/checkm_result
[2024-01-24 12:06:54,319] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:54,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:54,342] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:54,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:54,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016481285.1_ASM1648128v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:54,343] [INFO] Task started: Blastn
[2024-01-24 12:06:54,343] [INFO] Running command: blastn -query GCF_016481285.1_ASM1648128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6089642-cc36-4010-b96c-ed35b34767ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_016481285.1_ASM1648128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:55,157] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:55,162] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:55,162] [INFO] Target genome list was writen to GCF_016481285.1_ASM1648128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:55,174] [INFO] Task started: fastANI
[2024-01-24 12:06:55,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2b7bfc8-93d3-4fc2-a44a-509b819bd157/GCF_016481285.1_ASM1648128v1_genomic.fna.gz --refList GCF_016481285.1_ASM1648128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016481285.1_ASM1648128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:00,230] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:00,243] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:00,243] [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_016481285.1	s__Streptococcus zalophi	100.0	518	518	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_016481305.1	s__Streptococcus pacificus	87.9121	447	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380045.1	s__Streptococcus marimammalium	87.4481	410	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186445.1	s__Streptococcus agalactiae	78.4549	87	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_002096435.1	s__Streptococcus oralis_AA	78.3761	58	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.40	98.81	0.98	0.95	3	-
GCF_900475415.1	s__Streptococcus porcinus	78.2908	88	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_000187935.1	s__Streptococcus parauberis	78.2263	87	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_901542335.1	s__Streptococcus porcinus_A	78.2058	82	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_016461705.1	s__Streptococcus vicugnae	78.182	102	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_900104225.1	s__Streptococcus equinus_D	78.1744	92	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188055.2	s__Streptococcus urinalis	77.9774	106	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_018448765.1	s__Streptococcus oralis_BM	77.9035	67	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431045.1	s__Streptococcus orisasini	77.5748	84	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411475.1	s__Streptococcus sp000411475	77.4749	68	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,245] [INFO] GTDB search result was written to GCF_016481285.1_ASM1648128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:00,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:00,250] [INFO] DFAST_QC result json was written to GCF_016481285.1_ASM1648128v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:00,251] [INFO] DFAST_QC completed!
[2024-01-24 12:07:00,251] [INFO] Total running time: 0h0m35s