[2024-01-24 14:47:19,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference
[2024-01-24 14:47:21,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,125] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,126] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a610f1-2364-4afc-a3b3-e8b6835210f9/GCF_003987565.1_ASM398756v1_genomic.fna.gz | prodigal -d GCF_003987565.1_ASM398756v1_genomic.fna/cds.fna -a GCF_003987565.1_ASM398756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:25,300] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:25,301] [INFO] Task started: HMMsearch
[2024-01-24 14:47:25,301] [INFO] Running command: hmmsearch --tblout GCF_003987565.1_ASM398756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/reference_markers.hmm GCF_003987565.1_ASM398756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:25,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:25,533] [INFO] Found 6/6 markers.
[2024-01-24 14:47:25,556] [INFO] Query marker FASTA was written to GCF_003987565.1_ASM398756v1_genomic.fna/markers.fasta
[2024-01-24 14:47:25,556] [INFO] Task started: Blastn
[2024-01-24 14:47:25,557] [INFO] Running command: blastn -query GCF_003987565.1_ASM398756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/reference_markers.fasta -out GCF_003987565.1_ASM398756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:26,191] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:26,195] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:26,196] [INFO] Target genome list was writen to GCF_003987565.1_ASM398756v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:26,210] [INFO] Task started: fastANI
[2024-01-24 14:47:26,210] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a610f1-2364-4afc-a3b3-e8b6835210f9/GCF_003987565.1_ASM398756v1_genomic.fna.gz --refList GCF_003987565.1_ASM398756v1_genomic.fna/target_genomes.txt --output GCF_003987565.1_ASM398756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:39,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:39,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:39,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:39,724] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:39,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:39,724] [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 fessus	strain=CCUG 41755	GCA_003987565.1	120370	120370	type	True	100.0	748	748	95	conclusive
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	80.1417	184	748	95	below_threshold
Vagococcus zengguangii	strain=MN-17	GCA_005145005.1	2571750	2571750	type	True	78.8583	108	748	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.7926	105	748	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	78.7436	104	748	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.413	97	748	95	below_threshold
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	78.3741	70	748	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	78.3	155	748	95	below_threshold
Enterococcus quebecensis	strain=LMG 26306	GCA_001730365.1	903983	903983	type	True	78.2814	71	748	95	below_threshold
Enterococcus aquimarinus	strain=DSM 17690	GCA_001885765.1	328396	328396	type	True	78.2478	53	748	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	78.1279	116	748	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	78.0101	58	748	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	77.9433	88	748	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	77.9106	71	748	95	below_threshold
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	77.8578	97	748	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	77.806	127	748	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	77.5617	81	748	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	77.551	79	748	95	below_threshold
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	77.4775	87	748	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	77.1536	69	748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:39,730] [INFO] DFAST Taxonomy check result was written to GCF_003987565.1_ASM398756v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:39,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:39,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:39,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/checkm_data
[2024-01-24 14:47:39,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:39,758] [INFO] Task started: CheckM
[2024-01-24 14:47:39,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987565.1_ASM398756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987565.1_ASM398756v1_genomic.fna/checkm_input GCF_003987565.1_ASM398756v1_genomic.fna/checkm_result
[2024-01-24 14:48:00,643] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:00,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:00,661] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:00,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:00,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987565.1_ASM398756v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:00,662] [INFO] Task started: Blastn
[2024-01-24 14:48:00,662] [INFO] Running command: blastn -query GCF_003987565.1_ASM398756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0f23215-2fdd-481e-b2ea-73ce107b7b6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987565.1_ASM398756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:01,494] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:01,498] [INFO] Selected 25 target genomes.
[2024-01-24 14:48:01,498] [INFO] Target genome list was writen to GCF_003987565.1_ASM398756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:01,522] [INFO] Task started: fastANI
[2024-01-24 14:48:01,523] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a610f1-2364-4afc-a3b3-e8b6835210f9/GCF_003987565.1_ASM398756v1_genomic.fna.gz --refList GCF_003987565.1_ASM398756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987565.1_ASM398756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:14,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:14,429] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:14,430] [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_003987565.1	s__Vagococcus_D fessus	100.0	748	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011303955.1	s__Vagococcus_D coleopterorum	80.2499	184	748	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_005145005.1	s__Vagococcus_A zengguangii	78.8583	108	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.48	99.48	0.96	0.96	2	-
GCF_017829975.1	s__Vagococcus_D sp017829975	78.7394	104	748	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_001742285.1	s__Enterococcus rivorum	78.3741	70	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001730365.1	s__Enterococcus quebecensis	78.3333	70	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	78.291	157	748	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_017316185.1	s__Vagococcus sp017316185	78.262	94	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397115.1	s__Vagococcus carniphilus	78.1241	116	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000407445.1	s__Enterococcus moraviensis	78.0967	79	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002141365.1	s__Enterococcus sp002141365	78.0163	81	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635985.1	s__Enterococcus_I alcedinis	78.0101	58	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004795745.1	s__Vagococcus silagei	77.9433	88	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950325.1	s__Vagococcus_C humatus	77.8857	96	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885945.1	s__Enterococcus_A hermanniensis	77.8816	58	748	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_011304195.1	s__Vagococcus hydrophili	77.806	127	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258435.1	s__Carnobacterium divergens_A	77.6249	78	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.21	98.87	0.95	0.92	17	-
GCF_017315945.1	s__Enterococcus_B sp017315945	77.6217	69	748	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_001886265.1	s__Enterococcus_B thailandicus	77.551	79	748	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_000744375.1	s__Carnobacterium gallinarum	77.4775	87	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654945.1	s__JAATGB01 sp015654945	77.3855	54	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__JAATGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990225.1	s__Enterococcus_B villorum	77.1536	69	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:14,432] [INFO] GTDB search result was written to GCF_003987565.1_ASM398756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:14,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:14,443] [INFO] DFAST_QC result json was written to GCF_003987565.1_ASM398756v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:14,444] [INFO] DFAST_QC completed!
[2024-01-24 14:48:14,444] [INFO] Total running time: 0h0m55s