[2024-01-24 11:26:38,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference
[2024-01-24 11:26:40,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,307] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg775464e9-5467-4a4f-87a3-59fcd4fb3cae/GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna.gz | prodigal -d GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/cds.fna -a GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,931] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,932] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,932] [INFO] Running command: hmmsearch --tblout GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/reference_markers.hmm GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,185] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,213] [INFO] Query marker FASTA was written to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/markers.fasta
[2024-01-24 11:26:45,213] [INFO] Task started: Blastn
[2024-01-24 11:26:45,213] [INFO] Running command: blastn -query GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/markers.fasta -db /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/reference_markers.fasta -out GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:45,832] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:45,835] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:45,835] [INFO] Target genome list was writen to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/target_genomes.txt
[2024-01-24 11:26:45,874] [INFO] Task started: fastANI
[2024-01-24 11:26:45,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg775464e9-5467-4a4f-87a3-59fcd4fb3cae/GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna.gz --refList GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/target_genomes.txt --output GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:52,955] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:52,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:52,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:52,968] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:52,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:52,969] [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 bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	100.0	799	801	95	conclusive
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	84.8093	543	801	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	84.6515	574	801	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	78.8941	251	801	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.8341	219	801	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	78.7587	215	801	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	78.2821	146	801	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	78.2252	65	801	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	78.0615	92	801	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.0317	90	801	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	77.9222	88	801	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.7877	62	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:52,970] [INFO] DFAST Taxonomy check result was written to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/tc_result.tsv
[2024-01-24 11:26:52,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:52,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:52,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/checkm_data
[2024-01-24 11:26:52,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:52,999] [INFO] Task started: CheckM
[2024-01-24 11:26:52,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/checkm_input GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/checkm_result
[2024-01-24 11:27:14,318] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:14,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,342] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:14,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:14,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/markers.fasta)
[2024-01-24 11:27:14,344] [INFO] Task started: Blastn
[2024-01-24 11:27:14,344] [INFO] Running command: blastn -query GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/markers.fasta -db /var/lib/cwl/stgb571fd5d-72e1-487e-ae92-510070a41f16/dqc_reference/reference_markers_gtdb.fasta -out GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:15,115] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:15,118] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:15,118] [INFO] Target genome list was writen to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:15,128] [INFO] Task started: fastANI
[2024-01-24 11:27:15,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg775464e9-5467-4a4f-87a3-59fcd4fb3cae/GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna.gz --refList GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/target_genomes_gtdb.txt --output GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:20,189] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:20,204] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:20,205] [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_003950315.1	s__Vagococcus bubulae	100.0	799	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003462485.1	s__Vagococcus sp003462485	89.5575	565	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001870205.1	s__Vagococcus teuberi	84.8144	542	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_002026305.1	s__Vagococcus martis	84.5917	577	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
GCF_017316185.1	s__Vagococcus sp017316185	79.3572	211	801	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	78.8892	253	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337315.1	s__Vagococcus fluvialis	78.8533	218	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_011304195.1	s__Vagococcus hydrophili	78.4905	205	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163795.1	s__Vagococcus fluvialis_A	78.3534	198	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011303955.1	s__Vagococcus_D coleopterorum	78.2579	65	801	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,206] [INFO] GTDB search result was written to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:20,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:20,210] [INFO] DFAST_QC result json was written to GCF_003950315.1_Vagococcus_bubulae_SS1994T_genomic.fna/dqc_result.json
[2024-01-24 11:27:20,210] [INFO] DFAST_QC completed!
[2024-01-24 11:27:20,210] [INFO] Total running time: 0h0m41s