[2024-01-24 14:11:46,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference
[2024-01-24 14:11:47,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,895] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgdea55432-8d01-4b09-a1fc-30b84e35b82b/GCF_000376985.1_ASM37698v1_genomic.fna.gz | prodigal -d GCF_000376985.1_ASM37698v1_genomic.fna/cds.fna -a GCF_000376985.1_ASM37698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:53,042] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:53,042] [INFO] Task started: HMMsearch
[2024-01-24 14:11:53,043] [INFO] Running command: hmmsearch --tblout GCF_000376985.1_ASM37698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/reference_markers.hmm GCF_000376985.1_ASM37698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:53,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:53,286] [INFO] Found 6/6 markers.
[2024-01-24 14:11:53,312] [INFO] Query marker FASTA was written to GCF_000376985.1_ASM37698v1_genomic.fna/markers.fasta
[2024-01-24 14:11:53,312] [INFO] Task started: Blastn
[2024-01-24 14:11:53,312] [INFO] Running command: blastn -query GCF_000376985.1_ASM37698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/reference_markers.fasta -out GCF_000376985.1_ASM37698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:53,903] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:53,907] [INFO] Selected 28 target genomes.
[2024-01-24 14:11:53,908] [INFO] Target genome list was writen to GCF_000376985.1_ASM37698v1_genomic.fna/target_genomes.txt
[2024-01-24 14:11:54,052] [INFO] Task started: fastANI
[2024-01-24 14:11:54,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea55432-8d01-4b09-a1fc-30b84e35b82b/GCF_000376985.1_ASM37698v1_genomic.fna.gz --refList GCF_000376985.1_ASM37698v1_genomic.fna/target_genomes.txt --output GCF_000376985.1_ASM37698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:03,611] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:03,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:03,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:03,636] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:03,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:03,636] [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 henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	100.0	787	791	95	conclusive
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	80.1168	98	791	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	80.071	207	791	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	79.927	213	791	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	79.9181	214	791	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	79.6311	149	791	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	79.5827	87	791	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	79.5673	265	791	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	79.4686	203	791	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.2307	109	791	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	79.122	247	791	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	79.1131	216	791	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	79.1087	245	791	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	79.0964	219	791	95	below_threshold
Streptococcus varani	strain=FF10	GCA_001375655.1	1608583	1608583	type	True	78.97	138	791	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9015	123	791	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	78.8845	215	791	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.8642	224	791	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	78.8623	84	791	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	78.8305	201	791	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	78.6829	99	791	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	78.5344	102	791	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.5137	95	791	95	below_threshold
Streptococcus pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	78.5003	102	791	95	below_threshold
Streptococcus mutans	strain=NCTC10449	GCA_900475095.1	1309	1309	type	True	78.2256	127	791	95	below_threshold
Streptococcus mutans	strain=ATCC 25175	GCA_000347875.1	1309	1309	type	True	78.2174	126	791	95	below_threshold
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	78.1913	122	791	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.819	127	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:03,639] [INFO] DFAST Taxonomy check result was written to GCF_000376985.1_ASM37698v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:03,640] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:03,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:03,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/checkm_data
[2024-01-24 14:12:03,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:03,679] [INFO] Task started: CheckM
[2024-01-24 14:12:03,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376985.1_ASM37698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376985.1_ASM37698v1_genomic.fna/checkm_input GCF_000376985.1_ASM37698v1_genomic.fna/checkm_result
[2024-01-24 14:12:27,402] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:27,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:27,450] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:27,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:27,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376985.1_ASM37698v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:27,451] [INFO] Task started: Blastn
[2024-01-24 14:12:27,451] [INFO] Running command: blastn -query GCF_000376985.1_ASM37698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg181ff7ae-26aa-4cb5-abb3-0309d1c34432/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376985.1_ASM37698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:28,498] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:28,501] [INFO] Selected 19 target genomes.
[2024-01-24 14:12:28,501] [INFO] Target genome list was writen to GCF_000376985.1_ASM37698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:28,521] [INFO] Task started: fastANI
[2024-01-24 14:12:28,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea55432-8d01-4b09-a1fc-30b84e35b82b/GCF_000376985.1_ASM37698v1_genomic.fna.gz --refList GCF_000376985.1_ASM37698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376985.1_ASM37698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:36,016] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:36,036] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:36,036] [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_000376985.1	s__Streptococcus henryi	100.0	787	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	conclusive
GCA_000283635.1	s__Streptococcus macedonicus	80.2974	232	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_000154985.1	s__Streptococcus infantarius	79.9181	214	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_000380105.1	s__Streptococcus orisratti	79.5663	265	791	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	79.4686	203	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101445.1	s__Streptococcus equinus_B	79.2937	209	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	79.1392	200	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475675.1	s__Streptococcus lutetiensis	79.1387	217	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_900104225.1	s__Streptococcus equinus_D	79.0797	203	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375655.1	s__Streptococcus varani	78.9691	139	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594605.1	s__Streptococcus sp015594605	78.9564	205	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379985.1	s__Streptococcus caballi	78.8845	215	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	78.8642	224	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_000187265.1	s__Streptococcus equinus	78.8518	200	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
GCF_000380005.1	s__Streptococcus didelphis	78.6829	99	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901542335.1	s__Streptococcus porcinus_A	78.6248	103	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_011421455.1	s__Streptococcus catagoni	78.564	96	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_006739205.1	s__Streptococcus mutans	78.2573	125	791	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	-
GCF_002355215.1	s__Streptococcus troglodytae	77.7932	128	791	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 14:12:36,038] [INFO] GTDB search result was written to GCF_000376985.1_ASM37698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:36,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:36,044] [INFO] DFAST_QC result json was written to GCF_000376985.1_ASM37698v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:36,045] [INFO] DFAST_QC completed!
[2024-01-24 14:12:36,045] [INFO] Total running time: 0h0m49s