[2024-01-24 13:25:44,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:44,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:44,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference
[2024-01-24 13:25:46,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:46,091] [INFO] Task started: Prodigal
[2024-01-24 13:25:46,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg5456a487-7aa3-4ac7-b96c-7e74000444b8/GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna.gz | prodigal -d GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/cds.fna -a GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:52,006] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:52,007] [INFO] Task started: HMMsearch
[2024-01-24 13:25:52,007] [INFO] Running command: hmmsearch --tblout GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/reference_markers.hmm GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:52,269] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:52,271] [INFO] Found 6/6 markers.
[2024-01-24 13:25:52,298] [INFO] Query marker FASTA was written to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/markers.fasta
[2024-01-24 13:25:52,299] [INFO] Task started: Blastn
[2024-01-24 13:25:52,299] [INFO] Running command: blastn -query GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/reference_markers.fasta -out GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:52,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:52,938] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:52,939] [INFO] Target genome list was writen to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:52,971] [INFO] Task started: fastANI
[2024-01-24 13:25:52,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg5456a487-7aa3-4ac7-b96c-7e74000444b8/GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna.gz --refList GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/target_genomes.txt --output GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:01,358] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:01,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:01,371] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:01,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:01,371] [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 saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	99.9941	874	878	95	conclusive
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	99.9923	862	878	95	conclusive
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	99.9665	830	878	95	conclusive
Enterococcus columbae	strain=ATCC 51263	GCA_000406925.1	1355	1355	type	True	79.2257	162	878	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	79.0334	143	878	95	below_threshold
Enterococcus columbae	strain=ATCC 51263	GCA_000407225.1	1355	1355	type	True	78.8394	149	878	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	78.3169	192	878	95	below_threshold
Tetragenococcus halophilus subsp. halophilus	strain=DSM 20339	GCA_003841405.1	1513897	51669	type	True	78.0704	122	878	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.9876	127	878	95	below_threshold
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	77.8671	119	878	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	77.6516	134	878	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.576	80	878	95	below_threshold
Tetragenococcus halophilus subsp. flandriensis	strain=DSM 23766	GCA_002922845.1	1513898	51669	type	True	77.0097	130	878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,373] [INFO] DFAST Taxonomy check result was written to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:01,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:01,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:01,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/checkm_data
[2024-01-24 13:26:01,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:01,402] [INFO] Task started: CheckM
[2024-01-24 13:26:01,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/checkm_input GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/checkm_result
[2024-01-24 13:26:25,580] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:25,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:25,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:25,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:25,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/markers.fasta)
[2024-01-24 13:26:25,608] [INFO] Task started: Blastn
[2024-01-24 13:26:25,608] [INFO] Running command: blastn -query GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3155a592-c6ed-4aea-a6a6-c652a501cd1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:26,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:26,395] [INFO] Selected 14 target genomes.
[2024-01-24 13:26:26,395] [INFO] Target genome list was writen to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:26,407] [INFO] Task started: fastANI
[2024-01-24 13:26:26,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg5456a487-7aa3-4ac7-b96c-7e74000444b8/GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna.gz --refList GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:33,269] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:33,287] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:33,287] [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_000407285.1	s__Enterococcus_F saccharolyticus	99.9923	862	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_017426705.1	s__Enterococcus_F sp017426705	85.235	696	878	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_009933335.1	s__Enterococcus_F sp009933335	80.2394	420	878	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_000406925.1	s__Enterococcus_E columbae	79.1964	163	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	99.98	99.97	1.00	0.99	4	-
GCF_016909125.1	s__Enterococcus_I lemanii	78.2997	187	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.21	98.21	0.88	0.88	2	-
GCF_003841405.1	s__Tetragenococcus halophilus	78.101	121	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	97.86	96.17	0.89	0.79	30	-
GCA_019116505.1	s__Enterococcus_I avicola	78.0841	156	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730365.1	s__Enterococcus quebecensis	78.0145	128	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001465345.1	s__Enterococcus rotai	78.0137	130	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001297065.1	s__Enterococcus_D sp001297065	78.0032	147	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCA_015680865.1	s__Enterococcus_B lacertideformus	77.7075	136	878	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_009933175.1	s__Enterococcus_B sp009933175	77.7027	144	878	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_007990225.1	s__Enterococcus_B villorum	77.676	133	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
GCF_000423785.1	s__Tetragenococcus muriaticus	76.8774	102	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	98.93	98.87	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,289] [INFO] GTDB search result was written to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:33,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:33,293] [INFO] DFAST_QC result json was written to GCF_000407005.1_Ente_sacc_ATCC43076_V1_genomic.fna/dqc_result.json
[2024-01-24 13:26:33,294] [INFO] DFAST_QC completed!
[2024-01-24 13:26:33,294] [INFO] Total running time: 0h0m48s