[2024-01-24 15:26:04,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference
[2024-01-24 15:26:07,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,022] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg82eeea88-254d-46ea-b0ae-ddb98ef6e5fd/GCF_900187085.1_50624_E01_genomic.fna.gz | prodigal -d GCF_900187085.1_50624_E01_genomic.fna/cds.fna -a GCF_900187085.1_50624_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:12,541] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:12,541] [INFO] Task started: HMMsearch
[2024-01-24 15:26:12,542] [INFO] Running command: hmmsearch --tblout GCF_900187085.1_50624_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/reference_markers.hmm GCF_900187085.1_50624_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:12,825] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:12,827] [INFO] Found 6/6 markers.
[2024-01-24 15:26:12,854] [INFO] Query marker FASTA was written to GCF_900187085.1_50624_E01_genomic.fna/markers.fasta
[2024-01-24 15:26:12,854] [INFO] Task started: Blastn
[2024-01-24 15:26:12,855] [INFO] Running command: blastn -query GCF_900187085.1_50624_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/reference_markers.fasta -out GCF_900187085.1_50624_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:14,793] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:14,798] [INFO] Selected 21 target genomes.
[2024-01-24 15:26:14,798] [INFO] Target genome list was writen to GCF_900187085.1_50624_E01_genomic.fna/target_genomes.txt
[2024-01-24 15:26:14,809] [INFO] Task started: fastANI
[2024-01-24 15:26:14,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg82eeea88-254d-46ea-b0ae-ddb98ef6e5fd/GCF_900187085.1_50624_E01_genomic.fna.gz --refList GCF_900187085.1_50624_E01_genomic.fna/target_genomes.txt --output GCF_900187085.1_50624_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:23,509] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:23,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:23,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:23,527] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:26:23,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:23,528] [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 merionis	strain=NCTC13788	GCA_900187085.1	400065	400065	type	True	100.0	793	794	95	conclusive
Streptococcus merionis	strain=DSM 19192	GCA_000380085.1	400065	400065	type	True	99.9671	772	794	95	conclusive
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	80.2809	70	794	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	79.6248	70	794	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.5244	64	794	95	below_threshold
Streptococcus timonensis	strain=Marseille-P2915	GCA_900095845.1	1852387	1852387	type	True	79.3834	84	794	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.2811	89	794	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.2011	86	794	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	78.9669	68	794	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	78.4435	65	794	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	78.2967	110	794	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.0327	78	794	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	77.9564	84	794	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	77.8676	84	794	95	below_threshold
Streptococcus ovuberis	strain=CCUG 69612	GCA_012396585.1	1936207	1936207	type	True	77.8313	156	794	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	77.7912	88	794	95	below_threshold
Streptococcus entericus	strain=DSM 14446	GCA_000380025.1	155680	155680	type	True	77.7745	83	794	95	below_threshold
Streptococcus azizii	strain=12-5202	GCA_001984715.1	1579424	1579424	type	True	77.768	86	794	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	77.7385	83	794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:23,529] [INFO] DFAST Taxonomy check result was written to GCF_900187085.1_50624_E01_genomic.fna/tc_result.tsv
[2024-01-24 15:26:23,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:23,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:23,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/checkm_data
[2024-01-24 15:26:23,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:23,561] [INFO] Task started: CheckM
[2024-01-24 15:26:23,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187085.1_50624_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187085.1_50624_E01_genomic.fna/checkm_input GCF_900187085.1_50624_E01_genomic.fna/checkm_result
[2024-01-24 15:26:47,397] [INFO] Task succeeded: CheckM
[2024-01-24 15:26:47,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:26:47,419] [INFO] ===== Completeness check finished =====
[2024-01-24 15:26:47,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:26:47,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187085.1_50624_E01_genomic.fna/markers.fasta)
[2024-01-24 15:26:47,420] [INFO] Task started: Blastn
[2024-01-24 15:26:47,420] [INFO] Running command: blastn -query GCF_900187085.1_50624_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fbe1007-eb63-4bc3-9b63-ede2f38de762/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187085.1_50624_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:48,416] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:48,423] [INFO] Selected 26 target genomes.
[2024-01-24 15:26:48,423] [INFO] Target genome list was writen to GCF_900187085.1_50624_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:26:48,448] [INFO] Task started: fastANI
[2024-01-24 15:26:48,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg82eeea88-254d-46ea-b0ae-ddb98ef6e5fd/GCF_900187085.1_50624_E01_genomic.fna.gz --refList GCF_900187085.1_50624_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187085.1_50624_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:26:58,435] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:58,455] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:26:58,456] [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_000380085.1	s__Streptococcus merionis	99.9671	772	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009738225.1	s__Streptococcus sp001556435	80.0278	66	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCF_000785515.1	s__Streptococcus salivarius	79.7865	73	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	-
GCF_900095845.1	s__Streptococcus timonensis	79.5692	84	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002355895.1	s__Streptococcus sp002355895	79.4928	80	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902159415.1	s__Streptococcus mitis_BG	79.088	62	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	78.9067	69	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294495.1	s__Streptococcus suis	78.6056	107	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	98.55	95.80	0.92	0.80	1267	-
GCA_905221145.1	s__Streptococcus sp905221145	78.3919	72	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380125.1	s__Streptococcus ovis	78.2967	110	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221085.1	s__Streptococcus sp905221085	78.1451	79	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	78.063	86	794	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	78.0256	98	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_013277415.1	s__Streptococcus sp013277415	77.9848	88	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.52	95.41	0.90	0.87	4	-
GCF_002962445.1	s__Streptococcus suis_V	77.9463	92	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.67	95.20	0.83	0.80	11	-
GCF_000440115.1	s__Streptococcus suis_L	77.8892	104	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860865.1	s__Streptococcus mitis_AT	77.8751	87	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.74	95.72	0.90	0.90	3	-
GCF_001070715.1	s__Streptococcus pseudopneumoniae_H	77.8513	95	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396585.1	s__Streptococcus ovuberis	77.8313	156	794	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	77.8191	100	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.81	98.81	0.93	0.93	2	-
GCA_000440235.1	s__Streptococcus suis_F	77.7799	101	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.62	95.22	0.78	0.75	8	-
GCF_000380025.1	s__Streptococcus entericus	77.7618	82	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380105.1	s__Streptococcus orisratti	77.7135	84	794	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	77.6423	97	794	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	77.3347	76	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002436115.1	s__Streptococcus sp002436115	76.7759	68	794	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 15:26:58,458] [INFO] GTDB search result was written to GCF_900187085.1_50624_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:26:58,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:26:58,463] [INFO] DFAST_QC result json was written to GCF_900187085.1_50624_E01_genomic.fna/dqc_result.json
[2024-01-24 15:26:58,464] [INFO] DFAST_QC completed!
[2024-01-24 15:26:58,464] [INFO] Total running time: 0h0m54s