[2024-01-24 13:31:33,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference
[2024-01-24 13:31:34,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,684] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bbcafc0-81c8-4fc4-8b69-b2b001cc675a/GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna.gz | prodigal -d GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/cds.fna -a GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:42,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:42,529] [INFO] Task started: HMMsearch
[2024-01-24 13:31:42,529] [INFO] Running command: hmmsearch --tblout GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/reference_markers.hmm GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:42,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:42,833] [INFO] Found 6/6 markers.
[2024-01-24 13:31:42,864] [INFO] Query marker FASTA was written to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/markers.fasta
[2024-01-24 13:31:42,864] [INFO] Task started: Blastn
[2024-01-24 13:31:42,864] [INFO] Running command: blastn -query GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/reference_markers.fasta -out GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:43,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:43,532] [INFO] Selected 14 target genomes.
[2024-01-24 13:31:43,533] [INFO] Target genome list was writen to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/target_genomes.txt
[2024-01-24 13:31:43,539] [INFO] Task started: fastANI
[2024-01-24 13:31:43,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbcafc0-81c8-4fc4-8b69-b2b001cc675a/GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna.gz --refList GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/target_genomes.txt --output GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:53,420] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:53,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:53,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:53,432] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:31:53,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:53,432] [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 moraviensis	strain=ATCC BAA-383	GCA_000407445.1	155617	155617	type	True	100.0	1191	1192	95	conclusive
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	99.9828	1190	1192	95	conclusive
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	99.9658	1168	1192	95	conclusive
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	84.9413	797	1192	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	84.4921	799	1192	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	84.464	809	1192	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	84.1322	758	1192	95	below_threshold
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	83.7553	822	1192	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	83.3681	852	1192	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.5219	244	1192	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	77.7882	154	1192	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.68	150	1192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:53,434] [INFO] DFAST Taxonomy check result was written to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/tc_result.tsv
[2024-01-24 13:31:53,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:53,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:53,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/checkm_data
[2024-01-24 13:31:53,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:53,479] [INFO] Task started: CheckM
[2024-01-24 13:31:53,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/checkm_input GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/checkm_result
[2024-01-24 13:32:23,378] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:23,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:23,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:23,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:23,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/markers.fasta)
[2024-01-24 13:32:23,406] [INFO] Task started: Blastn
[2024-01-24 13:32:23,406] [INFO] Running command: blastn -query GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a0c9d25-322f-4d53-97ea-e79c36b19ad6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:24,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:24,184] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:24,184] [INFO] Target genome list was writen to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:24,190] [INFO] Task started: fastANI
[2024-01-24 13:32:24,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbcafc0-81c8-4fc4-8b69-b2b001cc675a/GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna.gz --refList GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:33,675] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:33,686] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:33,686] [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_000407445.1	s__Enterococcus moraviensis	100.0	1191	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_001465345.1	s__Enterococcus rotai	84.9598	796	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	84.4796	800	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_002148425.1	s__Enterococcus sp002148425	84.3895	786	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_001730295.1	s__Enterococcus plantarum	84.1322	758	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_001730285.1	s__Enterococcus ureasiticus	83.7553	822	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCA_001465115.1	s__Enterococcus silesiacus	83.7027	839	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002141365.1	s__Enterococcus sp002141365	83.5047	835	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407145.1	s__Enterococcus caccae	83.3776	794	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_000633635.1	s__Enterococcus crotali	83.3519	853	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_017377505.1	s__Enterococcus sp017377505	83.2096	755	1192	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:33,687] [INFO] GTDB search result was written to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:33,688] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:33,691] [INFO] DFAST_QC result json was written to GCF_000407445.1_Ente_mora_BAA-383_V2_genomic.fna/dqc_result.json
[2024-01-24 13:32:33,691] [INFO] DFAST_QC completed!
[2024-01-24 13:32:33,691] [INFO] Total running time: 0h1m0s