[2024-01-24 11:52:04,811] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference
[2024-01-24 11:52:06,051] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:06,052] [INFO] Task started: Prodigal
[2024-01-24 11:52:06,052] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc9beff3-ba26-42fe-bec0-ee6324e097c2/GCF_001885985.1_ASM188598v1_genomic.fna.gz | prodigal -d GCF_001885985.1_ASM188598v1_genomic.fna/cds.fna -a GCF_001885985.1_ASM188598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:12,898] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:12,899] [INFO] Task started: HMMsearch
[2024-01-24 11:52:12,899] [INFO] Running command: hmmsearch --tblout GCF_001885985.1_ASM188598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/reference_markers.hmm GCF_001885985.1_ASM188598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:13,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:13,158] [INFO] Found 6/6 markers.
[2024-01-24 11:52:13,191] [INFO] Query marker FASTA was written to GCF_001885985.1_ASM188598v1_genomic.fna/markers.fasta
[2024-01-24 11:52:13,192] [INFO] Task started: Blastn
[2024-01-24 11:52:13,192] [INFO] Running command: blastn -query GCF_001885985.1_ASM188598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/reference_markers.fasta -out GCF_001885985.1_ASM188598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:13,810] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:13,814] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:13,815] [INFO] Target genome list was writen to GCF_001885985.1_ASM188598v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:13,920] [INFO] Task started: fastANI
[2024-01-24 11:52:13,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc9beff3-ba26-42fe-bec0-ee6324e097c2/GCF_001885985.1_ASM188598v1_genomic.fna.gz --refList GCF_001885985.1_ASM188598v1_genomic.fna/target_genomes.txt --output GCF_001885985.1_ASM188598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:23,073] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:23,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:23,090] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:52:23,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:23,091] [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 haemoperoxidus	strain=DSM 15920	GCA_001885985.1	155618	155618	type	True	100.0	1140	1140	95	conclusive
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	99.9969	1140	1140	95	conclusive
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	99.9898	1139	1140	95	conclusive
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	86.5969	836	1140	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	85.5287	757	1140	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	85.1938	821	1140	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	83.6192	758	1140	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	82.4956	692	1140	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.4899	239	1140	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.2022	139	1140	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.5497	124	1140	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.3014	89	1140	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.0234	120	1140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,092] [INFO] DFAST Taxonomy check result was written to GCF_001885985.1_ASM188598v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:23,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:23,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:23,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/checkm_data
[2024-01-24 11:52:23,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:23,132] [INFO] Task started: CheckM
[2024-01-24 11:52:23,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001885985.1_ASM188598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001885985.1_ASM188598v1_genomic.fna/checkm_input GCF_001885985.1_ASM188598v1_genomic.fna/checkm_result
[2024-01-24 11:52:49,950] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:49,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:49,975] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:49,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:49,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001885985.1_ASM188598v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:49,976] [INFO] Task started: Blastn
[2024-01-24 11:52:49,976] [INFO] Running command: blastn -query GCF_001885985.1_ASM188598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f982c80-86fa-4566-bc16-0fa19c5750db/dqc_reference/reference_markers_gtdb.fasta -out GCF_001885985.1_ASM188598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:50,741] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:50,745] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:50,745] [INFO] Target genome list was writen to GCF_001885985.1_ASM188598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:50,759] [INFO] Task started: fastANI
[2024-01-24 11:52:50,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc9beff3-ba26-42fe-bec0-ee6324e097c2/GCF_001885985.1_ASM188598v1_genomic.fna.gz --refList GCF_001885985.1_ASM188598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001885985.1_ASM188598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:59,609] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:59,621] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:59,621] [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_000407165.1	s__Enterococcus haemoperoxidus	99.9969	1140	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	conclusive
GCF_001730285.1	s__Enterococcus ureasiticus	86.5918	837	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_001730295.1	s__Enterococcus plantarum	85.5322	757	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCA_001465115.1	s__Enterococcus silesiacus	85.1485	852	1140	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	84.8877	822	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_002141365.1	s__Enterococcus sp002141365	84.757	851	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633635.1	s__Enterococcus crotali	84.4911	843	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_000407145.1	s__Enterococcus caccae	84.3444	839	1140	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	83.7896	738	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_001730365.1	s__Enterococcus quebecensis	82.5684	699	1140	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:59,623] [INFO] GTDB search result was written to GCF_001885985.1_ASM188598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:59,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:59,628] [INFO] DFAST_QC result json was written to GCF_001885985.1_ASM188598v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:59,628] [INFO] DFAST_QC completed!
[2024-01-24 11:52:59,628] [INFO] Total running time: 0h0m55s