[2024-01-24 13:13:12,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference
[2024-01-24 13:13:13,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,767] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg54ffac7f-d421-4b07-a2f3-b22f2f3ce3ac/GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna.gz | prodigal -d GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/cds.fna -a GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:18,165] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:18,165] [INFO] Task started: HMMsearch
[2024-01-24 13:13:18,165] [INFO] Running command: hmmsearch --tblout GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/reference_markers.hmm GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:18,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:18,461] [INFO] Found 6/6 markers.
[2024-01-24 13:13:18,489] [INFO] Query marker FASTA was written to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/markers.fasta
[2024-01-24 13:13:18,490] [INFO] Task started: Blastn
[2024-01-24 13:13:18,490] [INFO] Running command: blastn -query GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/markers.fasta -db /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/reference_markers.fasta -out GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:19,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:19,117] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:19,117] [INFO] Target genome list was writen to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/target_genomes.txt
[2024-01-24 13:13:19,444] [INFO] Task started: fastANI
[2024-01-24 13:13:19,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ffac7f-d421-4b07-a2f3-b22f2f3ce3ac/GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna.gz --refList GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/target_genomes.txt --output GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:31,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:31,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:31,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:31,161] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:31,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:31,161] [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 vulneris	strain=SS1995	GCA_003950515.1	1977869	1977869	type	True	100.0	759	763	95	conclusive
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	78.9146	249	763	95	below_threshold
Vagococcus penaei	strain=LMG 24833	GCA_003987515.1	633807	633807	type	True	78.8835	247	763	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	78.6373	151	763	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	78.5634	135	763	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	78.1458	153	763	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	77.9416	59	763	95	below_threshold
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	77.6979	72	763	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	77.6967	73	763	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	77.5959	60	763	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	77.5732	144	763	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	77.4224	74	763	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	77.396	54	763	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	77.3826	69	763	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_001886035.1	53346	53346	type	True	77.0954	52	763	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	76.8658	63	763	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	76.7606	59	763	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	76.6599	62	763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:31,163] [INFO] DFAST Taxonomy check result was written to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/tc_result.tsv
[2024-01-24 13:13:31,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:31,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:31,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/checkm_data
[2024-01-24 13:13:31,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:31,195] [INFO] Task started: CheckM
[2024-01-24 13:13:31,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/checkm_input GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/checkm_result
[2024-01-24 13:13:52,756] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:52,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:52,774] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:52,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:52,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/markers.fasta)
[2024-01-24 13:13:52,776] [INFO] Task started: Blastn
[2024-01-24 13:13:52,776] [INFO] Running command: blastn -query GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/markers.fasta -db /var/lib/cwl/stg58dfcede-f40b-4762-a648-ded1b1440e35/dqc_reference/reference_markers_gtdb.fasta -out GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:53,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:53,507] [INFO] Selected 20 target genomes.
[2024-01-24 13:13:53,507] [INFO] Target genome list was writen to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:53,552] [INFO] Task started: fastANI
[2024-01-24 13:13:53,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ffac7f-d421-4b07-a2f3-b22f2f3ce3ac/GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna.gz --refList GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/target_genomes_gtdb.txt --output GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:03,119] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,135] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:03,135] [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_003950515.1	s__Vagococcus vulneris	100.0	759	763	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_001998885.1	s__Vagococcus penaei	78.8982	250	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004792515.1	s__Vagococcus_A sp004792515	78.7478	76	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003337315.1	s__Vagococcus fluvialis	78.6391	150	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_003950315.1	s__Vagococcus bubulae	78.4481	139	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795745.1	s__Vagococcus silagei	78.1004	155	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002141365.1	s__Enterococcus sp002141365	78.0168	56	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.9844	69	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011397115.1	s__Enterococcus_C saigonensis	77.9416	59	763	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_001730305.1	s__Enterococcus termitis	77.6967	73	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002140715.1	s__Enterococcus sp002140715	77.6551	80	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730295.1	s__Enterococcus plantarum	77.5959	60	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_900163795.1	s__Vagococcus fluvialis_A	77.5898	172	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011304195.1	s__Vagococcus hydrophili	77.5732	144	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407445.1	s__Enterococcus moraviensis	77.5272	72	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000407605.1	s__Enterococcus_G sulfureus	77.5083	61	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_G	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000633635.1	s__Enterococcus crotali	77.4224	74	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_002813755.1	s__Enterococcus_B mundtii	77.396	54	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCF_001730365.1	s__Enterococcus quebecensis	77.2922	79	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003957375.1	s__Enterococcus_B mundtii_C	77.0189	52	763	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.247	99.65	99.65	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,137] [INFO] GTDB search result was written to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:03,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:03,141] [INFO] DFAST_QC result json was written to GCF_003950515.1_Vagococcus_vulneris_SS1995T_genomic.fna/dqc_result.json
[2024-01-24 13:14:03,141] [INFO] DFAST_QC completed!
[2024-01-24 13:14:03,141] [INFO] Total running time: 0h0m51s