[2024-01-25 17:49:50,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference
[2024-01-25 17:49:51,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,710] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg0998c479-8a45-4db4-ab97-78a0e47dc61a/GCF_900447655.1_51485_G01_genomic.fna.gz | prodigal -d GCF_900447655.1_51485_G01_genomic.fna/cds.fna -a GCF_900447655.1_51485_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:00,562] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:00,563] [INFO] Task started: HMMsearch
[2024-01-25 17:50:00,563] [INFO] Running command: hmmsearch --tblout GCF_900447655.1_51485_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/reference_markers.hmm GCF_900447655.1_51485_G01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:00,834] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:00,835] [INFO] Found 6/6 markers.
[2024-01-25 17:50:00,874] [INFO] Query marker FASTA was written to GCF_900447655.1_51485_G01_genomic.fna/markers.fasta
[2024-01-25 17:50:00,875] [INFO] Task started: Blastn
[2024-01-25 17:50:00,875] [INFO] Running command: blastn -query GCF_900447655.1_51485_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/reference_markers.fasta -out GCF_900447655.1_51485_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:01,440] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:01,443] [INFO] Selected 12 target genomes.
[2024-01-25 17:50:01,443] [INFO] Target genome list was writen to GCF_900447655.1_51485_G01_genomic.fna/target_genomes.txt
[2024-01-25 17:50:01,450] [INFO] Task started: fastANI
[2024-01-25 17:50:01,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg0998c479-8a45-4db4-ab97-78a0e47dc61a/GCF_900447655.1_51485_G01_genomic.fna.gz --refList GCF_900447655.1_51485_G01_genomic.fna/target_genomes.txt --output GCF_900447655.1_51485_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:11,614] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:11,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:11,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:11,621] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 17:50:11,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:11,622] [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 avium	strain=NCTC9938	GCA_900447655.1	33945	33945	type	True	100.0	1558	1559	95	conclusive
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	99.9955	1529	1559	95	conclusive
Enterococcus avium	strain=ATCC 14025	GCA_000406965.1	33945	33945	type	True	99.9602	1534	1559	95	conclusive
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	99.9133	1401	1559	95	conclusive
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	81.8833	828	1559	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	81.6906	820	1559	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	81.2221	664	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:11,623] [INFO] DFAST Taxonomy check result was written to GCF_900447655.1_51485_G01_genomic.fna/tc_result.tsv
[2024-01-25 17:50:11,624] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:11,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:11,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/checkm_data
[2024-01-25 17:50:11,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:11,671] [INFO] Task started: CheckM
[2024-01-25 17:50:11,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447655.1_51485_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447655.1_51485_G01_genomic.fna/checkm_input GCF_900447655.1_51485_G01_genomic.fna/checkm_result
[2024-01-25 17:50:42,085] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:42,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:42,102] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:42,102] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:42,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447655.1_51485_G01_genomic.fna/markers.fasta)
[2024-01-25 17:50:42,103] [INFO] Task started: Blastn
[2024-01-25 17:50:42,103] [INFO] Running command: blastn -query GCF_900447655.1_51485_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg756474f1-ece0-4ae2-8bcc-ab942b28c32d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447655.1_51485_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:42,872] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:42,875] [INFO] Selected 13 target genomes.
[2024-01-25 17:50:42,875] [INFO] Target genome list was writen to GCF_900447655.1_51485_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:42,887] [INFO] Task started: fastANI
[2024-01-25 17:50:42,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg0998c479-8a45-4db4-ab97-78a0e47dc61a/GCF_900447655.1_51485_G01_genomic.fna.gz --refList GCF_900447655.1_51485_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447655.1_51485_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:53,838] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:53,847] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:53,847] [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_000406965.1	s__Enterococcus_A avium	99.9602	1534	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	conclusive
GCF_018917525.1	s__Enterococcus_A raffinosus_A	91.7483	1143	1559	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_000407185.1	s__Enterococcus_A malodoratus	82.111	849	1559	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_001886185.1	s__Enterococcus_A raffinosus	82.0675	746	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.27	97.96	0.91	0.87	12	-
GCF_005405485.1	s__Enterococcus_A hulanensis	81.6701	823	1559	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	81.4635	791	1559	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	81.3017	664	1559	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_005405205.1	s__Enterococcus_A pingfangensis	81.2429	400	1559	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	81.1162	361	1559	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_001544295.1	s__Enterococcus_A pseudoavium	81.0504	522	1559	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_005405365.1	s__Enterococcus_A xiangfangensis	80.9624	475	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.65	99.31	0.96	0.92	3	-
GCF_005405345.1	s__Enterococcus_A viikkiensis	80.6173	437	1559	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	80.33	533	1559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.13	98.05	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:53,848] [INFO] GTDB search result was written to GCF_900447655.1_51485_G01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:53,849] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:53,852] [INFO] DFAST_QC result json was written to GCF_900447655.1_51485_G01_genomic.fna/dqc_result.json
[2024-01-25 17:50:53,852] [INFO] DFAST_QC completed!
[2024-01-25 17:50:53,852] [INFO] Total running time: 0h1m3s