[2024-01-24 12:29:27,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:27,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:27,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference
[2024-01-24 12:29:28,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,809] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg88ba8fab-1e70-4a63-b2f1-1c179b71e704/GCF_021654455.1_ASM2165445v1_genomic.fna.gz | prodigal -d GCF_021654455.1_ASM2165445v1_genomic.fna/cds.fna -a GCF_021654455.1_ASM2165445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:34,020] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:34,021] [INFO] Task started: HMMsearch
[2024-01-24 12:29:34,021] [INFO] Running command: hmmsearch --tblout GCF_021654455.1_ASM2165445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/reference_markers.hmm GCF_021654455.1_ASM2165445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:34,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:34,386] [INFO] Found 6/6 markers.
[2024-01-24 12:29:34,422] [INFO] Query marker FASTA was written to GCF_021654455.1_ASM2165445v1_genomic.fna/markers.fasta
[2024-01-24 12:29:34,422] [INFO] Task started: Blastn
[2024-01-24 12:29:34,423] [INFO] Running command: blastn -query GCF_021654455.1_ASM2165445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/reference_markers.fasta -out GCF_021654455.1_ASM2165445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:35,011] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:35,015] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:35,015] [INFO] Target genome list was writen to GCF_021654455.1_ASM2165445v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:35,020] [INFO] Task started: fastANI
[2024-01-24 12:29:35,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg88ba8fab-1e70-4a63-b2f1-1c179b71e704/GCF_021654455.1_ASM2165445v1_genomic.fna.gz --refList GCF_021654455.1_ASM2165445v1_genomic.fna/target_genomes.txt --output GCF_021654455.1_ASM2165445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:41,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:41,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:41,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:41,244] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:41,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:41,245] [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 parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	100.0	732	732	95	conclusive
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	87.3459	439	732	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	87.237	444	732	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	82.5443	143	732	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	82.0777	149	732	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.6563	123	732	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.513	239	732	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	80.0943	300	732	95	below_threshold
Streptococcus equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	80.0699	93	732	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.3127	141	732	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	79.1845	83	732	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	78.7867	160	732	95	below_threshold
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	78.6263	156	732	95	below_threshold
Streptococcus azizii	strain=12-5202	GCA_001984715.1	1579424	1579424	type	True	78.1873	145	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:41,250] [INFO] DFAST Taxonomy check result was written to GCF_021654455.1_ASM2165445v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:41,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:41,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:41,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/checkm_data
[2024-01-24 12:29:41,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:41,293] [INFO] Task started: CheckM
[2024-01-24 12:29:41,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654455.1_ASM2165445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654455.1_ASM2165445v1_genomic.fna/checkm_input GCF_021654455.1_ASM2165445v1_genomic.fna/checkm_result
[2024-01-24 12:30:05,157] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:05,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:05,188] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:05,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:05,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654455.1_ASM2165445v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:05,190] [INFO] Task started: Blastn
[2024-01-24 12:30:05,190] [INFO] Running command: blastn -query GCF_021654455.1_ASM2165445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg904e8c6c-e33b-4148-947d-d4af2f4bed73/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654455.1_ASM2165445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:06,148] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:06,152] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:06,152] [INFO] Target genome list was writen to GCF_021654455.1_ASM2165445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:06,161] [INFO] Task started: fastANI
[2024-01-24 12:30:06,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg88ba8fab-1e70-4a63-b2f1-1c179b71e704/GCF_021654455.1_ASM2165445v1_genomic.fna.gz --refList GCF_021654455.1_ASM2165445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654455.1_ASM2165445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:12,955] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:12,965] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:12,966] [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_000440555.1	s__Streptococcus suis_N	97.0469	592	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.61	95.42	0.83	0.79	5	conclusive
GCF_004283785.1	s__Streptococcus parasuis	94.803	491	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_000294495.1	s__Streptococcus suis	87.1768	446	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	98.55	95.80	0.92	0.80	1267	-
GCF_902702775.1	s__Streptococcus suis_W	87.1018	465	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_016743335.1	s__Streptococcus suis_Y	86.4585	426	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.53	95.45	0.79	0.78	5	-
GCA_002831545.1	s__Streptococcus suis_P	86.4103	460	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.04	0.87	0.78	133	-
GCF_000440115.1	s__Streptococcus suis_L	86.3298	416	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_002760245.1	s__Streptococcus suis_I	86.2741	425	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	84.9707	393	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_016775005.1	s__Streptococcus suis_X	84.4562	334	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_002964575.1	s__Streptococcus suis_R	84.3383	405	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	84.0987	401	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:12,967] [INFO] GTDB search result was written to GCF_021654455.1_ASM2165445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:12,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:12,971] [INFO] DFAST_QC result json was written to GCF_021654455.1_ASM2165445v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:12,971] [INFO] DFAST_QC completed!
[2024-01-24 12:30:12,972] [INFO] Total running time: 0h0m46s