[2024-01-24 13:17:27,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference
[2024-01-24 13:17:28,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,319] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2ff41eb-554f-423d-9e69-fcb9c7902218/GCF_000294495.1_ASM29449v1_genomic.fna.gz | prodigal -d GCF_000294495.1_ASM29449v1_genomic.fna/cds.fna -a GCF_000294495.1_ASM29449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,123] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,124] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,124] [INFO] Running command: hmmsearch --tblout GCF_000294495.1_ASM29449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/reference_markers.hmm GCF_000294495.1_ASM29449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,367] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,387] [INFO] Query marker FASTA was written to GCF_000294495.1_ASM29449v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,387] [INFO] Task started: Blastn
[2024-01-24 13:17:33,387] [INFO] Running command: blastn -query GCF_000294495.1_ASM29449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/reference_markers.fasta -out GCF_000294495.1_ASM29449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:33,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:33,994] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:33,994] [INFO] Target genome list was writen to GCF_000294495.1_ASM29449v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:33,998] [INFO] Task started: fastANI
[2024-01-24 13:17:33,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ff41eb-554f-423d-9e69-fcb9c7902218/GCF_000294495.1_ASM29449v1_genomic.fna.gz --refList GCF_000294495.1_ASM29449v1_genomic.fna/target_genomes.txt --output GCF_000294495.1_ASM29449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:38,779] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:38,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:38,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:38,793] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:38,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:38,793] [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 suis	strain=S735	GCA_000294495.1	1307	1307	type	True	100.0	658	660	95	conclusive
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	99.998	657	660	95	conclusive
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	87.2418	451	660	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	83.0845	171	660	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	82.4583	142	660	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.9851	270	660	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	80.8512	362	660	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	78.9245	98	660	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.8544	127	660	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	78.7477	172	660	95	below_threshold
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	78.5311	185	660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:38,795] [INFO] DFAST Taxonomy check result was written to GCF_000294495.1_ASM29449v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:38,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:38,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:38,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/checkm_data
[2024-01-24 13:17:38,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:38,824] [INFO] Task started: CheckM
[2024-01-24 13:17:38,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000294495.1_ASM29449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000294495.1_ASM29449v1_genomic.fna/checkm_input GCF_000294495.1_ASM29449v1_genomic.fna/checkm_result
[2024-01-24 13:18:00,415] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:00,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:00,435] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:00,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:00,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000294495.1_ASM29449v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:00,436] [INFO] Task started: Blastn
[2024-01-24 13:18:00,436] [INFO] Running command: blastn -query GCF_000294495.1_ASM29449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg647d4688-1f5f-43d9-957c-4d24cf208731/dqc_reference/reference_markers_gtdb.fasta -out GCF_000294495.1_ASM29449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:01,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:01,364] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:01,364] [INFO] Target genome list was writen to GCF_000294495.1_ASM29449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:01,372] [INFO] Task started: fastANI
[2024-01-24 13:18:01,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ff41eb-554f-423d-9e69-fcb9c7902218/GCF_000294495.1_ASM29449v1_genomic.fna.gz --refList GCF_000294495.1_ASM29449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000294495.1_ASM29449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:07,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:07,436] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:18:07,437] [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_000294495.1	s__Streptococcus suis	100.0	659	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	98.55	95.80	0.92	0.80	1267	inconclusive
GCF_902702775.1	s__Streptococcus suis_W	95.2627	552	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	96.52	95.78	0.85	0.77	106	inconclusive
GCA_002831545.1	s__Streptococcus suis_P	94.6885	551	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.04	0.87	0.78	133	-
GCA_000440235.1	s__Streptococcus suis_F	94.5536	528	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.62	95.22	0.78	0.75	8	-
GCF_002760245.1	s__Streptococcus suis_I	94.3923	501	660	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	94.3521	511	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.53	95.45	0.79	0.78	5	-
GCF_000440115.1	s__Streptococcus suis_L	93.0937	510	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964575.1	s__Streptococcus suis_R	86.9766	455	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000440555.1	s__Streptococcus suis_N	86.5887	432	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.61	95.42	0.83	0.79	5	-
GCF_016775005.1	s__Streptococcus suis_X	86.4942	373	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	97.65	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:07,438] [INFO] GTDB search result was written to GCF_000294495.1_ASM29449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:07,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:07,441] [INFO] DFAST_QC result json was written to GCF_000294495.1_ASM29449v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:07,441] [INFO] DFAST_QC completed!
[2024-01-24 13:18:07,441] [INFO] Total running time: 0h0m40s