[2024-01-25 19:41:20,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:20,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:20,703] [INFO] DQC Reference Directory: /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference
[2024-01-25 19:41:21,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:21,826] [INFO] Task started: Prodigal
[2024-01-25 19:41:21,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a267eaf-566e-4806-b395-f15b04c3b5c8/GCF_029143285.1_ASM2914328v1_genomic.fna.gz | prodigal -d GCF_029143285.1_ASM2914328v1_genomic.fna/cds.fna -a GCF_029143285.1_ASM2914328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:25,537] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:25,537] [INFO] Task started: HMMsearch
[2024-01-25 19:41:25,537] [INFO] Running command: hmmsearch --tblout GCF_029143285.1_ASM2914328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/reference_markers.hmm GCF_029143285.1_ASM2914328v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:25,787] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:25,788] [INFO] Found 6/6 markers.
[2024-01-25 19:41:25,809] [INFO] Query marker FASTA was written to GCF_029143285.1_ASM2914328v1_genomic.fna/markers.fasta
[2024-01-25 19:41:25,809] [INFO] Task started: Blastn
[2024-01-25 19:41:25,810] [INFO] Running command: blastn -query GCF_029143285.1_ASM2914328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/reference_markers.fasta -out GCF_029143285.1_ASM2914328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:26,367] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:26,370] [INFO] Selected 25 target genomes.
[2024-01-25 19:41:26,370] [INFO] Target genome list was writen to GCF_029143285.1_ASM2914328v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:26,399] [INFO] Task started: fastANI
[2024-01-25 19:41:26,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a267eaf-566e-4806-b395-f15b04c3b5c8/GCF_029143285.1_ASM2914328v1_genomic.fna.gz --refList GCF_029143285.1_ASM2914328v1_genomic.fna/target_genomes.txt --output GCF_029143285.1_ASM2914328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:36,850] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:36,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:36,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:36,865] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:41:36,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:41:36,865] [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
Vagococcus fessus	strain=CCUG 41755	GCA_003987565.1	120370	120370	type	True	90.3578	618	773	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	79.9057	177	773	95	below_threshold
Vagococcus zengguangii	strain=MN-17	GCA_005145005.1	2571750	2571750	type	True	78.6341	95	773	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	78.387	153	773	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	78.2795	104	773	95	below_threshold
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	78.2771	83	773	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.0521	108	773	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	77.8093	121	773	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	77.7931	115	773	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	77.7895	116	773	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000407505.1	154621	154621	type	True	77.5938	71	773	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	77.5772	73	773	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	77.5669	72	773	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	77.5285	72	773	95	below_threshold
Isobaculum melis	strain=DSM 13760	GCA_900111355.1	142588	142588	type	True	77.5234	78	773	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	77.4807	92	773	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.303	66	773	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.3008	59	773	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	77.2297	70	773	95	below_threshold
Enterococcus ureilyticus	strain=LMG 26676	GCA_001730315.1	1131292	1131292	type	True	77.2116	70	773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:36,867] [INFO] DFAST Taxonomy check result was written to GCF_029143285.1_ASM2914328v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:36,868] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:36,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:36,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/checkm_data
[2024-01-25 19:41:36,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:36,898] [INFO] Task started: CheckM
[2024-01-25 19:41:36,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029143285.1_ASM2914328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029143285.1_ASM2914328v1_genomic.fna/checkm_input GCF_029143285.1_ASM2914328v1_genomic.fna/checkm_result
[2024-01-25 19:41:53,838] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:53,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:53,856] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:53,856] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:53,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029143285.1_ASM2914328v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:53,857] [INFO] Task started: Blastn
[2024-01-25 19:41:53,857] [INFO] Running command: blastn -query GCF_029143285.1_ASM2914328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga40f946a-7903-4802-83a6-a86699808f56/dqc_reference/reference_markers_gtdb.fasta -out GCF_029143285.1_ASM2914328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:54,646] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:54,649] [INFO] Selected 23 target genomes.
[2024-01-25 19:41:54,649] [INFO] Target genome list was writen to GCF_029143285.1_ASM2914328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:54,675] [INFO] Task started: fastANI
[2024-01-25 19:41:54,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a267eaf-566e-4806-b395-f15b04c3b5c8/GCF_029143285.1_ASM2914328v1_genomic.fna.gz --refList GCF_029143285.1_ASM2914328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029143285.1_ASM2914328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:05,466] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:05,478] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:42:05,478] [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_003987565.1	s__Vagococcus_D fessus	90.3321	619	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303955.1	s__Vagococcus_D coleopterorum	79.9057	177	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	78.387	153	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	98.18	98.18	0.88	0.88	2	-
GCF_001870205.1	s__Vagococcus teuberi	78.2771	83	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_004792515.1	s__Vagococcus_A sp004792515	78.0523	108	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003337315.1	s__Vagococcus fluvialis	77.7931	115	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_003462485.1	s__Vagococcus sp003462485	77.7899	83	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011304195.1	s__Vagococcus hydrophili	77.7815	122	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742285.1	s__Enterococcus rivorum	77.6588	78	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001885765.1	s__Enterococcus_I aquimarinus	77.6532	57	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.10	98.04	0.96	0.95	6	-
GCF_900111355.1	s__Isobaculum melis	77.5604	78	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Isobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407505.1	s__Enterococcus_B phoeniculicola	77.5496	72	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001886265.1	s__Enterococcus_B thailandicus	77.5285	72	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_900163795.1	s__Vagococcus fluvialis_A	77.492	114	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003950315.1	s__Vagococcus bubulae	77.4807	92	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730315.1	s__Enterococcus ureilyticus	77.2116	70	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.1103	81	773	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_000746825.1	s__Carnobacterium_A inhibens	76.9533	62	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:05,480] [INFO] GTDB search result was written to GCF_029143285.1_ASM2914328v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:05,480] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:05,484] [INFO] DFAST_QC result json was written to GCF_029143285.1_ASM2914328v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:05,484] [INFO] DFAST_QC completed!
[2024-01-25 19:42:05,484] [INFO] Total running time: 0h0m45s