[2024-01-24 11:51:23,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,862] [INFO] DQC Reference Directory: /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference
[2024-01-24 11:51:25,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,188] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg203b581d-7754-4d96-9fad-34f5a6fdc507/GCF_003987595.1_ASM398759v1_genomic.fna.gz | prodigal -d GCF_003987595.1_ASM398759v1_genomic.fna/cds.fna -a GCF_003987595.1_ASM398759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:30,404] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:30,405] [INFO] Task started: HMMsearch
[2024-01-24 11:51:30,405] [INFO] Running command: hmmsearch --tblout GCF_003987595.1_ASM398759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/reference_markers.hmm GCF_003987595.1_ASM398759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:30,627] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:30,628] [INFO] Found 6/6 markers.
[2024-01-24 11:51:30,667] [INFO] Query marker FASTA was written to GCF_003987595.1_ASM398759v1_genomic.fna/markers.fasta
[2024-01-24 11:51:30,668] [INFO] Task started: Blastn
[2024-01-24 11:51:30,668] [INFO] Running command: blastn -query GCF_003987595.1_ASM398759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/reference_markers.fasta -out GCF_003987595.1_ASM398759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:31,261] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:31,270] [INFO] Selected 28 target genomes.
[2024-01-24 11:51:31,270] [INFO] Target genome list was writen to GCF_003987595.1_ASM398759v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:31,306] [INFO] Task started: fastANI
[2024-01-24 11:51:31,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg203b581d-7754-4d96-9fad-34f5a6fdc507/GCF_003987595.1_ASM398759v1_genomic.fna.gz --refList GCF_003987595.1_ASM398759v1_genomic.fna/target_genomes.txt --output GCF_003987595.1_ASM398759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:43,465] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:43,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:43,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:43,484] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:43,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:43,485] [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
Vagococcus entomophilus	strain=DSM 24756	GCA_003987595.1	1160095	1160095	type	True	100.0	812	812	95	conclusive
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	78.3596	58	812	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.3043	59	812	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	78.2535	60	812	95	below_threshold
Enterococcus hirae	strain=FDAARGOS_1123	GCA_016766815.1	1354	1354	type	True	78.2131	58	812	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	78.1772	58	812	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	78.1218	58	812	95	below_threshold
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	78.0045	80	812	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	77.992	80	812	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	77.8903	80	812	95	below_threshold
Enterococcus quebecensis	strain=LMG 26306	GCA_001730365.1	903983	903983	type	True	77.8213	69	812	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.7773	68	812	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	77.7465	65	812	95	below_threshold
Enterococcus cecorum	strain=ATCC 43198	GCA_000492155.1	44008	44008	type	True	77.6967	59	812	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	77.6877	52	812	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	77.6654	55	812	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	77.5661	68	812	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	77.5359	56	812	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.4478	61	812	95	below_threshold
Enterococcus cecorum	strain=DSM 20682	GCA_000379745.1	44008	44008	type	True	77.432	55	812	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	77.4181	69	812	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	77.3821	55	812	95	below_threshold
Enterococcus canintestini	strain=DSM 21207	GCA_001885735.1	317010	317010	type	True	77.3162	62	812	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.2515	76	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:43,487] [INFO] DFAST Taxonomy check result was written to GCF_003987595.1_ASM398759v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:43,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:43,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:43,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/checkm_data
[2024-01-24 11:51:43,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:43,514] [INFO] Task started: CheckM
[2024-01-24 11:51:43,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987595.1_ASM398759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987595.1_ASM398759v1_genomic.fna/checkm_input GCF_003987595.1_ASM398759v1_genomic.fna/checkm_result
[2024-01-24 11:52:06,639] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:06,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:06,664] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:06,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:06,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987595.1_ASM398759v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:06,665] [INFO] Task started: Blastn
[2024-01-24 11:52:06,665] [INFO] Running command: blastn -query GCF_003987595.1_ASM398759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49078516-3fe5-442c-b1ea-11f08501cc1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987595.1_ASM398759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:07,787] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:07,791] [INFO] Selected 27 target genomes.
[2024-01-24 11:52:07,791] [INFO] Target genome list was writen to GCF_003987595.1_ASM398759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:07,810] [INFO] Task started: fastANI
[2024-01-24 11:52:07,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg203b581d-7754-4d96-9fad-34f5a6fdc507/GCF_003987595.1_ASM398759v1_genomic.fna.gz --refList GCF_003987595.1_ASM398759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987595.1_ASM398759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:20,572] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:20,592] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:20,593] [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_003987595.1	s__Vagococcus_E entomophilus	100.0	812	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000271405.2	s__Enterococcus_B hirae	78.3043	59	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_017315945.1	s__Enterococcus_B sp017315945	78.2844	75	812	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_002947535.1	s__Enterococcus_B mundtii_B	77.9808	63	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	97.82	97.77	0.91	0.90	3	-
GCF_001730315.1	s__Enterococcus ureilyticus	77.975	78	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_001886265.1	s__Enterococcus_B thailandicus	77.935	79	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_001730365.1	s__Enterococcus quebecensis	77.8213	69	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.7485	64	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795745.1	s__Vagococcus silagei	77.7465	65	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407565.1	s__Enterococcus_E cecorum	77.7361	57	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	97.77	96.06	0.87	0.77	49	-
GCF_001730295.1	s__Enterococcus plantarum	77.7062	82	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_000407145.1	s__Enterococcus caccae	77.7041	81	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_011303955.1	s__Vagococcus_D coleopterorum	77.6717	53	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	77.646	54	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	98.18	98.18	0.88	0.88	2	-
GCF_002140715.1	s__Enterococcus sp002140715	77.6385	94	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002141365.1	s__Enterococcus sp002141365	77.6166	90	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745255.1	s__Enterococcus sp016745255	77.6009	58	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316125.1	s__Enterococcus_B sp017316125	77.5449	85	812	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_017829975.1	s__Vagococcus_D sp017829975	77.4478	61	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886195.1	s__Enterococcus_B ratti	77.4181	69	812	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_017377505.1	s__Enterococcus sp017377505	77.3427	85	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_001885735.1	s__Enterococcus_C canintestini	77.3162	62	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
GCF_014397115.1	s__Vagococcus carniphilus	77.2576	77	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900163795.1	s__Vagococcus fluvialis_A	76.8213	75	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:20,595] [INFO] GTDB search result was written to GCF_003987595.1_ASM398759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:20,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:20,601] [INFO] DFAST_QC result json was written to GCF_003987595.1_ASM398759v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:20,601] [INFO] DFAST_QC completed!
[2024-01-24 11:52:20,601] [INFO] Total running time: 0h0m57s