[2024-01-25 19:52:05,627] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference
[2024-01-25 19:52:06,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,766] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg0876d578-a3d9-4ed5-866c-0b7cda6d3ea3/GCF_022869705.1_ASM2286970v1_genomic.fna.gz | prodigal -d GCF_022869705.1_ASM2286970v1_genomic.fna/cds.fna -a GCF_022869705.1_ASM2286970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:12,138] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:12,138] [INFO] Task started: HMMsearch
[2024-01-25 19:52:12,138] [INFO] Running command: hmmsearch --tblout GCF_022869705.1_ASM2286970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/reference_markers.hmm GCF_022869705.1_ASM2286970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:12,366] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:12,367] [INFO] Found 6/6 markers.
[2024-01-25 19:52:12,392] [INFO] Query marker FASTA was written to GCF_022869705.1_ASM2286970v1_genomic.fna/markers.fasta
[2024-01-25 19:52:12,393] [INFO] Task started: Blastn
[2024-01-25 19:52:12,393] [INFO] Running command: blastn -query GCF_022869705.1_ASM2286970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/reference_markers.fasta -out GCF_022869705.1_ASM2286970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:12,967] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:12,970] [INFO] Selected 9 target genomes.
[2024-01-25 19:52:12,970] [INFO] Target genome list was writen to GCF_022869705.1_ASM2286970v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:12,980] [INFO] Task started: fastANI
[2024-01-25 19:52:12,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg0876d578-a3d9-4ed5-866c-0b7cda6d3ea3/GCF_022869705.1_ASM2286970v1_genomic.fna.gz --refList GCF_022869705.1_ASM2286970v1_genomic.fna/target_genomes.txt --output GCF_022869705.1_ASM2286970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:18,292] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:18,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:18,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:18,297] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:52:18,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:18,298] [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 faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	100.0	955	955	95	conclusive
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	99.9902	954	955	95	conclusive
Enterococcus faecalis	strain=NCTC 775	GCA_015311765.1	1351	1351	type	True	99.9645	922	955	95	conclusive
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	99.9603	928	955	95	conclusive
Enterococcus faecalis	strain=NCTC775	GCA_900447895.1	1351	1351	type	True	99.945	911	955	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:52:18,299] [INFO] DFAST Taxonomy check result was written to GCF_022869705.1_ASM2286970v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:18,300] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:18,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:18,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/checkm_data
[2024-01-25 19:52:18,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:18,338] [INFO] Task started: CheckM
[2024-01-25 19:52:18,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022869705.1_ASM2286970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022869705.1_ASM2286970v1_genomic.fna/checkm_input GCF_022869705.1_ASM2286970v1_genomic.fna/checkm_result
[2024-01-25 19:52:39,964] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:39,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:39,980] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:39,981] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:39,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022869705.1_ASM2286970v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:39,981] [INFO] Task started: Blastn
[2024-01-25 19:52:39,981] [INFO] Running command: blastn -query GCF_022869705.1_ASM2286970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg084f75d6-d269-47a5-a06b-8a0a70484bbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_022869705.1_ASM2286970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:40,757] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:40,760] [INFO] Selected 19 target genomes.
[2024-01-25 19:52:40,760] [INFO] Target genome list was writen to GCF_022869705.1_ASM2286970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:40,781] [INFO] Task started: fastANI
[2024-01-25 19:52:40,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg0876d578-a3d9-4ed5-866c-0b7cda6d3ea3/GCF_022869705.1_ASM2286970v1_genomic.fna.gz --refList GCF_022869705.1_ASM2286970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022869705.1_ASM2286970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:51,926] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:51,940] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:51,940] [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_000392875.1	s__Enterococcus faecalis	99.9902	955	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	conclusive
GCA_019116505.1	s__Enterococcus_I avicola	79.0573	88	955	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_001465345.1	s__Enterococcus rotai	78.9809	229	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148425.1	s__Enterococcus sp002148425	78.8229	241	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_002140715.1	s__Enterococcus sp002140715	78.7687	236	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	78.7205	221	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005405345.1	s__Enterococcus_A viikkiensis	78.6044	112	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407445.1	s__Enterococcus moraviensis	78.5299	254	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001730295.1	s__Enterococcus plantarum	78.4989	230	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_017830045.1	s__Enterococcus sp017830045	78.4666	116	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730365.1	s__Enterococcus quebecensis	78.4356	223	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001465115.1	s__Enterococcus silesiacus	78.3884	239	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017377505.1	s__Enterococcus sp017377505	78.3756	239	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_001730285.1	s__Enterococcus ureasiticus	78.3406	247	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_001742285.1	s__Enterococcus rivorum	78.3371	193	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000407145.1	s__Enterococcus caccae	78.2074	245	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001730315.1	s__Enterococcus ureilyticus	78.1074	226	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_007990225.1	s__Enterococcus_B villorum	77.8334	147	955	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_017426705.1	s__Enterococcus_F sp017426705	77.4761	156	955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:51,945] [INFO] GTDB search result was written to GCF_022869705.1_ASM2286970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:51,947] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:51,950] [INFO] DFAST_QC result json was written to GCF_022869705.1_ASM2286970v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:51,950] [INFO] DFAST_QC completed!
[2024-01-25 19:52:51,950] [INFO] Total running time: 0h0m46s