[2024-01-24 14:31:00,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,286] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/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/stg8153bacd-aa01-4668-a2ba-6c507f52d37e/GCF_018137985.1_ASM1813798v1_genomic.fna.gz | prodigal -d GCF_018137985.1_ASM1813798v1_genomic.fna/cds.fna -a GCF_018137985.1_ASM1813798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:07,014] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:07,014] [INFO] Task started: HMMsearch
[2024-01-24 14:31:07,014] [INFO] Running command: hmmsearch --tblout GCF_018137985.1_ASM1813798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/reference_markers.hmm GCF_018137985.1_ASM1813798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:07,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:07,329] [INFO] Found 6/6 markers.
[2024-01-24 14:31:07,361] [INFO] Query marker FASTA was written to GCF_018137985.1_ASM1813798v1_genomic.fna/markers.fasta
[2024-01-24 14:31:07,362] [INFO] Task started: Blastn
[2024-01-24 14:31:07,362] [INFO] Running command: blastn -query GCF_018137985.1_ASM1813798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/reference_markers.fasta -out GCF_018137985.1_ASM1813798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:08,062] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:08,064] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:08,064] [INFO] Target genome list was writen to GCF_018137985.1_ASM1813798v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:08,078] [INFO] Task started: fastANI
[2024-01-24 14:31:08,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg8153bacd-aa01-4668-a2ba-6c507f52d37e/GCF_018137985.1_ASM1813798v1_genomic.fna.gz --refList GCF_018137985.1_ASM1813798v1_genomic.fna/target_genomes.txt --output GCF_018137985.1_ASM1813798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:13,023] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:13,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:13,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:13,036] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:13,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:13,036] [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 oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	100.0	728	732	95	conclusive
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	80.6631	279	732	95	below_threshold
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	80.6605	280	732	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	80.5065	239	732	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	80.1114	77	732	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	79.8724	127	732	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.0836	191	732	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.8379	120	732	95	below_threshold
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	78.6367	172	732	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	78.5141	176	732	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	78.4396	149	732	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.3367	107	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:13,037] [INFO] DFAST Taxonomy check result was written to GCF_018137985.1_ASM1813798v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:13,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:13,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:13,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/checkm_data
[2024-01-24 14:31:13,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:13,062] [INFO] Task started: CheckM
[2024-01-24 14:31:13,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018137985.1_ASM1813798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018137985.1_ASM1813798v1_genomic.fna/checkm_input GCF_018137985.1_ASM1813798v1_genomic.fna/checkm_result
[2024-01-24 14:31:33,320] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:33,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:33,336] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:33,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:33,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018137985.1_ASM1813798v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:33,337] [INFO] Task started: Blastn
[2024-01-24 14:31:33,337] [INFO] Running command: blastn -query GCF_018137985.1_ASM1813798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9573e68-b332-41c7-b4a8-f7c1409b9bcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_018137985.1_ASM1813798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:34,168] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:34,171] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:34,171] [INFO] Target genome list was writen to GCF_018137985.1_ASM1813798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:34,180] [INFO] Task started: fastANI
[2024-01-24 14:31:34,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg8153bacd-aa01-4668-a2ba-6c507f52d37e/GCF_018137985.1_ASM1813798v1_genomic.fna.gz --refList GCF_018137985.1_ASM1813798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018137985.1_ASM1813798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:40,652] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:40,662] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:40,663] [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_018137985.1	s__Streptococcus sp018137985	100.0	727	732	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_016775005.1	s__Streptococcus suis_X	81.0446	278	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	97.65	0.91	0.90	4	-
GCF_000440115.1	s__Streptococcus suis_L	80.8837	273	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964045.1	s__Streptococcus suis_U	80.8754	263	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_902702775.1	s__Streptococcus suis_W	80.8198	295	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	96.52	95.78	0.85	0.77	106	-
GCF_002760245.1	s__Streptococcus suis_I	80.8171	279	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960445.1	s__Streptococcus suis_O	80.7829	276	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423745.1	s__Streptococcus plurextorum	80.6768	125	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960625.1	s__Streptococcus suis_T	80.6406	283	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960425.1	s__Streptococcus suis_S	80.6054	283	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.81	98.81	0.93	0.93	2	-
GCF_002964575.1	s__Streptococcus suis_R	80.5943	289	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743335.1	s__Streptococcus suis_Y	80.4984	273	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.53	95.45	0.79	0.78	5	-
GCF_017601095.1	s__Streptococcus suis_Z	80.2674	259	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004283785.1	s__Streptococcus parasuis	80.2177	198	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.19	96.80	0.84	0.77	20	-
GCF_000440555.1	s__Streptococcus suis_N	80.2089	220	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.61	95.42	0.83	0.79	5	-
GCF_002962445.1	s__Streptococcus suis_V	79.9111	263	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.67	95.20	0.83	0.80	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,664] [INFO] GTDB search result was written to GCF_018137985.1_ASM1813798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:40,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:40,668] [INFO] DFAST_QC result json was written to GCF_018137985.1_ASM1813798v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:40,668] [INFO] DFAST_QC completed!
[2024-01-24 14:31:40,668] [INFO] Total running time: 0h0m40s