[2024-01-24 15:10:22,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference
[2024-01-24 15:10:24,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,216] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg729c2468-7049-473d-a9cf-38de3bd0e5eb/GCF_017874895.1_ASM1787489v1_genomic.fna.gz | prodigal -d GCF_017874895.1_ASM1787489v1_genomic.fna/cds.fna -a GCF_017874895.1_ASM1787489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:31,422] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:31,423] [INFO] Task started: HMMsearch
[2024-01-24 15:10:31,423] [INFO] Running command: hmmsearch --tblout GCF_017874895.1_ASM1787489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/reference_markers.hmm GCF_017874895.1_ASM1787489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:31,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:31,676] [INFO] Found 6/6 markers.
[2024-01-24 15:10:31,708] [INFO] Query marker FASTA was written to GCF_017874895.1_ASM1787489v1_genomic.fna/markers.fasta
[2024-01-24 15:10:31,709] [INFO] Task started: Blastn
[2024-01-24 15:10:31,709] [INFO] Running command: blastn -query GCF_017874895.1_ASM1787489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/reference_markers.fasta -out GCF_017874895.1_ASM1787489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:32,327] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:32,331] [INFO] Selected 26 target genomes.
[2024-01-24 15:10:32,331] [INFO] Target genome list was writen to GCF_017874895.1_ASM1787489v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:32,352] [INFO] Task started: fastANI
[2024-01-24 15:10:32,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg729c2468-7049-473d-a9cf-38de3bd0e5eb/GCF_017874895.1_ASM1787489v1_genomic.fna.gz --refList GCF_017874895.1_ASM1787489v1_genomic.fna/target_genomes.txt --output GCF_017874895.1_ASM1787489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:47,367] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:47,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:47,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:47,386] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:47,386] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:47,386] [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
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	99.9913	1212	1223	95	conclusive
Enterococcus quebecensis	strain=LMG 26306	GCA_001730365.1	903983	903983	type	True	78.7608	301	1223	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	78.6731	301	1223	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	78.5261	313	1223	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	78.5042	303	1223	95	below_threshold
Enterococcus haemoperoxidus	strain=DSM 15920	GCA_001885985.1	155618	155618	type	True	78.4816	301	1223	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	78.4449	287	1223	95	below_threshold
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	78.4363	284	1223	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	78.4051	307	1223	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000407445.1	155617	155617	type	True	78.3839	306	1223	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	78.3647	293	1223	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	78.3646	299	1223	95	below_threshold
Enterococcus caccae	strain=DSM 19114	GCA_001885825.1	317735	317735	type	True	78.3594	300	1223	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	78.3418	301	1223	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000394055.1	317735	317735	type	True	78.3189	300	1223	95	below_threshold
Enterococcus larvae	strain=BWM-S5	GCA_017830045.1	2794352	2794352	type	True	78.2783	133	1223	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	78.1689	305	1223	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	78.1043	192	1223	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.0603	194	1223	95	below_threshold
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	78.012	193	1223	95	below_threshold
Enterococcus faecalis	strain=NCTC 775	GCA_015311765.1	1351	1351	type	True	78.0041	192	1223	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	77.5626	80	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:47,389] [INFO] DFAST Taxonomy check result was written to GCF_017874895.1_ASM1787489v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:47,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:47,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:47,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/checkm_data
[2024-01-24 15:10:47,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:47,435] [INFO] Task started: CheckM
[2024-01-24 15:10:47,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874895.1_ASM1787489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874895.1_ASM1787489v1_genomic.fna/checkm_input GCF_017874895.1_ASM1787489v1_genomic.fna/checkm_result
[2024-01-24 15:11:14,839] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:14,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:14,871] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:14,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:14,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874895.1_ASM1787489v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:14,872] [INFO] Task started: Blastn
[2024-01-24 15:11:14,872] [INFO] Running command: blastn -query GCF_017874895.1_ASM1787489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49205d3b-88ec-4e32-8546-20322f60ba8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874895.1_ASM1787489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:15,719] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:15,723] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:15,723] [INFO] Target genome list was writen to GCF_017874895.1_ASM1787489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:15,735] [INFO] Task started: fastANI
[2024-01-24 15:11:15,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg729c2468-7049-473d-a9cf-38de3bd0e5eb/GCF_017874895.1_ASM1787489v1_genomic.fna.gz --refList GCF_017874895.1_ASM1787489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874895.1_ASM1787489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:27,367] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:27,383] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:27,384] [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_001742285.1	s__Enterococcus rivorum	99.9913	1212	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_001730365.1	s__Enterococcus quebecensis	78.7608	301	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002140715.1	s__Enterococcus sp002140715	78.6332	297	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	78.5386	312	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001730295.1	s__Enterococcus plantarum	78.5066	288	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_002141365.1	s__Enterococcus sp002141365	78.5053	309	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730305.1	s__Enterococcus termitis	78.4528	286	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002148425.1	s__Enterococcus sp002148425	78.3914	321	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_000407445.1	s__Enterococcus moraviensis	78.3713	307	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001730315.1	s__Enterococcus ureilyticus	78.3436	294	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_000407145.1	s__Enterococcus caccae	78.3418	301	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_017377505.1	s__Enterococcus sp017377505	78.276	305	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_001465345.1	s__Enterococcus rotai	78.1805	304	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009933175.1	s__Enterococcus_B sp009933175	78.1073	119	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000392875.1	s__Enterococcus faecalis	78.1034	192	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	-
GCA_019116505.1	s__Enterococcus_I avicola	77.6649	75	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.4138	118	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:27,387] [INFO] GTDB search result was written to GCF_017874895.1_ASM1787489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:27,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:27,392] [INFO] DFAST_QC result json was written to GCF_017874895.1_ASM1787489v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:27,393] [INFO] DFAST_QC completed!
[2024-01-24 15:11:27,393] [INFO] Total running time: 0h1m5s