[2024-01-24 13:41:25,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference
[2024-01-24 13:41:26,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:26,753] [INFO] Task started: Prodigal
[2024-01-24 13:41:26,754] [INFO] Running command: gunzip -c /var/lib/cwl/stga3744f41-01ba-4cf6-83a9-a63fdc8c2258/GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna.gz | prodigal -d GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/cds.fna -a GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:33,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:33,135] [INFO] Task started: HMMsearch
[2024-01-24 13:41:33,135] [INFO] Running command: hmmsearch --tblout GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/reference_markers.hmm GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:33,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:33,379] [INFO] Found 6/6 markers.
[2024-01-24 13:41:33,407] [INFO] Query marker FASTA was written to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/markers.fasta
[2024-01-24 13:41:33,407] [INFO] Task started: Blastn
[2024-01-24 13:41:33,407] [INFO] Running command: blastn -query GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/reference_markers.fasta -out GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:34,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:34,057] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:34,057] [INFO] Target genome list was writen to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:34,062] [INFO] Task started: fastANI
[2024-01-24 13:41:34,062] [INFO] Running command: fastANI --query /var/lib/cwl/stga3744f41-01ba-4cf6-83a9-a63fdc8c2258/GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna.gz --refList GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/target_genomes.txt --output GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:40,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:40,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:40,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:40,225] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:40,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:40,226] [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 dispar	strain=ATCC 51266	GCA_000407585.1	44009	44009	type	True	100.0	935	935	95	conclusive
Enterococcus dispar	strain=ATCC 51266	GCA_000406945.1	44009	44009	type	True	99.9881	931	935	95	conclusive
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	99.9477	884	935	95	conclusive
Enterococcus canintestini	strain=DSM 21207	GCA_001885735.1	317010	317010	type	True	86.3844	668	935	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	83.0942	618	935	95	below_threshold
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	80.1146	138	935	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	79.0498	122	935	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	78.7609	100	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:40,229] [INFO] DFAST Taxonomy check result was written to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:40,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:40,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:40,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/checkm_data
[2024-01-24 13:41:40,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:40,272] [INFO] Task started: CheckM
[2024-01-24 13:41:40,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/checkm_input GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/checkm_result
[2024-01-24 13:42:05,877] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:05,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:05,898] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:05,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:05,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/markers.fasta)
[2024-01-24 13:42:05,900] [INFO] Task started: Blastn
[2024-01-24 13:42:05,900] [INFO] Running command: blastn -query GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebad259-6957-4d48-9a03-96c1b00c340f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:06,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:06,743] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:06,744] [INFO] Target genome list was writen to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:06,753] [INFO] Task started: fastANI
[2024-01-24 13:42:06,753] [INFO] Running command: fastANI --query /var/lib/cwl/stga3744f41-01ba-4cf6-83a9-a63fdc8c2258/GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna.gz --refList GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:13,244] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,262] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:13,262] [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_000406945.1	s__Enterococcus_C dispar	99.9881	931	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	99.61	99.21	0.95	0.90	5	conclusive
GCF_001885735.1	s__Enterococcus_C canintestini	86.3844	668	935	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_017316025.1	s__Enterococcus_C sp017316025	83.475	652	935	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_011397115.1	s__Enterococcus_C saigonensis	83.0886	619	935	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_900604485.1	s__Enterococcus_C mediterraneensis	80.3289	139	935	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_017315945.1	s__Enterococcus_B sp017315945	80.0191	144	935	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_001544375.1	s__Enterococcus_H canis	79.1569	112	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_H	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002140915.1	s__Enterococcus_D sp002140915	78.6329	126	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909125.1	s__Enterococcus_I lemanii	78.2921	120	935	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_017316125.1	s__Enterococcus_B sp017316125	78.1314	142	935	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_009933335.1	s__Enterococcus_F sp009933335	77.8056	136	935	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_017426705.1	s__Enterococcus_F sp017426705	77.7534	160	935	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,264] [INFO] GTDB search result was written to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:13,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:13,269] [INFO] DFAST_QC result json was written to GCF_000407585.1_Ente_disp_ATCC51266_V2_genomic.fna/dqc_result.json
[2024-01-24 13:42:13,269] [INFO] DFAST_QC completed!
[2024-01-24 13:42:13,269] [INFO] Total running time: 0h0m48s