[2023-06-18 19:17:11,792] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:17:11,794] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:17:11,795] [INFO] DQC Reference Directory: /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference
[2023-06-18 19:17:13,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:13,024] [INFO] Task started: Prodigal
[2023-06-18 19:17:13,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg62ade2f0-d86a-47e2-8cca-f37b00a6e502/GCA_018376435.1_ASM1837643v1_genomic.fna.gz | prodigal -d GCA_018376435.1_ASM1837643v1_genomic.fna/cds.fna -a GCA_018376435.1_ASM1837643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:17:21,500] [INFO] Task succeeded: Prodigal
[2023-06-18 19:17:21,500] [INFO] Task started: HMMsearch
[2023-06-18 19:17:21,500] [INFO] Running command: hmmsearch --tblout GCA_018376435.1_ASM1837643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/reference_markers.hmm GCA_018376435.1_ASM1837643v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:17:21,738] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:17:21,739] [INFO] Found 6/6 markers.
[2023-06-18 19:17:21,781] [INFO] Query marker FASTA was written to GCA_018376435.1_ASM1837643v1_genomic.fna/markers.fasta
[2023-06-18 19:17:21,781] [INFO] Task started: Blastn
[2023-06-18 19:17:21,781] [INFO] Running command: blastn -query GCA_018376435.1_ASM1837643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/reference_markers.fasta -out GCA_018376435.1_ASM1837643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:22,355] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:22,359] [INFO] Selected 16 target genomes.
[2023-06-18 19:17:22,359] [INFO] Target genome list was writen to GCA_018376435.1_ASM1837643v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:22,363] [INFO] Task started: fastANI
[2023-06-18 19:17:22,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg62ade2f0-d86a-47e2-8cca-f37b00a6e502/GCA_018376435.1_ASM1837643v1_genomic.fna.gz --refList GCA_018376435.1_ASM1837643v1_genomic.fna/target_genomes.txt --output GCA_018376435.1_ASM1837643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:32,970] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:32,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:32,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:32,981] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 19:17:32,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 19:17:32,981] [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 raffinosus	strain=NBRC 100492	GCA_001544115.1	71452	71452	type	True	99.523	1204	1336	95	conclusive
Enterococcus raffinosus	strain=DSM 5633	GCA_001886185.1	71452	71452	type	True	99.4793	1214	1336	95	conclusive
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	82.5066	839	1336	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	82.1232	760	1336	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	82.1122	784	1336	95	below_threshold
Enterococcus avium	strain=NCTC9938	GCA_900447655.1	33945	33945	type	True	82.1108	792	1336	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	81.8764	796	1336	95	below_threshold
Enterococcus malodoratus	strain=NCTC12365	GCA_900447955.1	71451	71451	type	True	81.8657	809	1336	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	81.8335	802	1336	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	80.9551	643	1336	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	80.8949	362	1336	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	78.0884	186	1336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:17:32,983] [INFO] DFAST Taxonomy check result was written to GCA_018376435.1_ASM1837643v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:32,983] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:32,984] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:32,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/checkm_data
[2023-06-18 19:17:32,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:33,023] [INFO] Task started: CheckM
[2023-06-18 19:17:33,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376435.1_ASM1837643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376435.1_ASM1837643v1_genomic.fna/checkm_input GCA_018376435.1_ASM1837643v1_genomic.fna/checkm_result
[2023-06-18 19:18:03,626] [INFO] Task succeeded: CheckM
[2023-06-18 19:18:03,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:18:03,641] [INFO] ===== Completeness check finished =====
[2023-06-18 19:18:03,641] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:18:03,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376435.1_ASM1837643v1_genomic.fna/markers.fasta)
[2023-06-18 19:18:03,642] [INFO] Task started: Blastn
[2023-06-18 19:18:03,642] [INFO] Running command: blastn -query GCA_018376435.1_ASM1837643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e33052-b985-49d0-b9ae-0f2417a8a4ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376435.1_ASM1837643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:18:04,356] [INFO] Task succeeded: Blastn
[2023-06-18 19:18:04,360] [INFO] Selected 13 target genomes.
[2023-06-18 19:18:04,360] [INFO] Target genome list was writen to GCA_018376435.1_ASM1837643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:18:04,393] [INFO] Task started: fastANI
[2023-06-18 19:18:04,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg62ade2f0-d86a-47e2-8cca-f37b00a6e502/GCA_018376435.1_ASM1837643v1_genomic.fna.gz --refList GCA_018376435.1_ASM1837643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376435.1_ASM1837643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:18:14,396] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:14,408] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:18:14,408] [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_001886185.1	s__Enterococcus_A raffinosus	99.498	1213	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.27	97.96	0.91	0.87	12	conclusive
GCF_005405485.1	s__Enterococcus_A hulanensis	82.4891	841	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	97.15	97.02	0.83	0.81	4	-
GCF_017315985.1	s__Enterococcus_A sp017315985	82.0979	802	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000406965.1	s__Enterococcus_A avium	82.0261	790	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	-
GCF_000407185.1	s__Enterococcus_A malodoratus	81.8335	802	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.33	98.27	0.94	0.84	8	-
GCF_018917525.1	s__Enterococcus_A raffinosus_A	81.5309	764	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405205.1	s__Enterococcus_A pingfangensis	81.1611	402	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407545.1	s__Enterococcus_A gilvus	81.003	638	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.79	97.90	0.91	0.83	8	-
GCF_001544295.1	s__Enterococcus_A pseudoavium	80.9885	496	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405225.1	s__Enterococcus_A dongliensis	80.9055	361	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885905.1	s__Enterococcus_A devriesei	80.5965	506	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.13	98.05	0.88	0.86	3	-
GCF_005405345.1	s__Enterococcus_A viikkiensis	80.5217	442	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885945.1	s__Enterococcus_A hermanniensis	79.8061	405	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:18:14,410] [INFO] GTDB search result was written to GCA_018376435.1_ASM1837643v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:18:14,410] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:18:14,414] [INFO] DFAST_QC result json was written to GCA_018376435.1_ASM1837643v1_genomic.fna/dqc_result.json
[2023-06-18 19:18:14,414] [INFO] DFAST_QC completed!
[2023-06-18 19:18:14,414] [INFO] Total running time: 0h1m3s