[2024-01-25 18:39:35,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,657] [INFO] DQC Reference Directory: /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference
[2024-01-25 18:39:36,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,807] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0126ac9-cceb-4fbb-9c65-e7240a4afc04/GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna.gz | prodigal -d GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/cds.fna -a GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:41,215] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:41,216] [INFO] Task started: HMMsearch
[2024-01-25 18:39:41,216] [INFO] Running command: hmmsearch --tblout GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/reference_markers.hmm GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:41,444] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:41,446] [INFO] Found 6/6 markers.
[2024-01-25 18:39:41,466] [INFO] Query marker FASTA was written to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/markers.fasta
[2024-01-25 18:39:41,466] [INFO] Task started: Blastn
[2024-01-25 18:39:41,466] [INFO] Running command: blastn -query GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/reference_markers.fasta -out GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:42,029] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:42,032] [INFO] Selected 13 target genomes.
[2024-01-25 18:39:42,032] [INFO] Target genome list was writen to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/target_genomes.txt
[2024-01-25 18:39:42,039] [INFO] Task started: fastANI
[2024-01-25 18:39:42,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0126ac9-cceb-4fbb-9c65-e7240a4afc04/GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna.gz --refList GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/target_genomes.txt --output GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:47,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:47,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:47,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:47,714] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:39:47,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:39:47,715] [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 parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	94.223	581	668	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	94.1817	584	668	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	85.7141	409	668	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000222745.2	113107	113107	type	True	85.5584	416	668	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	85.5212	399	668	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	85.5198	416	668	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	85.3392	400	668	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	85.1009	409	668	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.8048	195	668	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	80.7804	205	668	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.7402	201	668	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.5025	120	668	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.3903	84	668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:47,716] [INFO] DFAST Taxonomy check result was written to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/tc_result.tsv
[2024-01-25 18:39:47,717] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:47,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:47,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/checkm_data
[2024-01-25 18:39:47,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:47,742] [INFO] Task started: CheckM
[2024-01-25 18:39:47,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/checkm_input GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/checkm_result
[2024-01-25 18:40:07,861] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:07,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:07,885] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:07,885] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:07,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/markers.fasta)
[2024-01-25 18:40:07,887] [INFO] Task started: Blastn
[2024-01-25 18:40:07,887] [INFO] Running command: blastn -query GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04ccd07-6e11-4ec9-b868-e33093c77156/dqc_reference/reference_markers_gtdb.fasta -out GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:08,746] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:08,748] [INFO] Selected 12 target genomes.
[2024-01-25 18:40:08,748] [INFO] Target genome list was writen to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:08,761] [INFO] Task started: fastANI
[2024-01-25 18:40:08,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0126ac9-cceb-4fbb-9c65-e7240a4afc04/GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna.gz --refList GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/target_genomes_gtdb.txt --output GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:17,572] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:17,580] [INFO] Found 12 fastANI hits (6 hits with ANI > circumscription radius)
[2024-01-25 18:40:17,581] [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
GCA_018366675.1	s__Streptococcus parasanguinis_E	95.6224	511	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.293	95.61	95.45	0.89	0.84	13	inconclusive
GCF_001813295.1	s__Streptococcus sp001813295	95.575	590	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2593	95.62	95.52	0.88	0.87	6	inconclusive
GCF_016648925.1	s__Streptococcus sp900766505	95.5576	587	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	inconclusive
GCF_009717815.1	s__Streptococcus parasanguinis_F	95.4961	595	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.25	95.86	95.53	0.89	0.86	10	inconclusive
GCF_000963275.1	s__Streptococcus parasanguinis_B	95.4777	599	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	inconclusive
GCF_001073155.1	s__Streptococcus parasanguinis_D	95.1996	553	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.84	96.67	0.91	0.89	4	inconclusive
GCF_000448565.1	s__Streptococcus sp000448565	95.0177	610	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2003	N/A	N/A	N/A	N/A	1	-
GCA_018365265.1	s__Streptococcus parasanguinis_G	94.8833	565	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0331	95.56	95.56	0.87	0.87	2	-
GCA_000180035.1	s__Streptococcus parasanguinis_C	94.8353	591	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.27	96.01	0.92	0.90	7	-
GCF_000164675.2	s__Streptococcus parasanguinis	94.1817	584	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.96	95.18	0.90	0.85	22	-
GCF_001074805.1	s__Streptococcus parasanguinis_A	94.1769	554	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373455.1	s__Streptococcus sp902373455	93.8668	315	668	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:17,582] [INFO] GTDB search result was written to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:17,583] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:17,587] [INFO] DFAST_QC result json was written to GCF_943193075.1_Streptococcus_sp_nov_DSM110150_genomic.fna/dqc_result.json
[2024-01-25 18:40:17,588] [INFO] DFAST_QC completed!
[2024-01-25 18:40:17,588] [INFO] Total running time: 0h0m42s