[2024-01-24 13:46:01,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,662] [INFO] DQC Reference Directory: /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference
[2024-01-24 13:46:03,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,154] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f3b1832-1898-4ace-964c-a90a45c3cdea/GCF_000270185.1_ASM27018v1_genomic.fna.gz | prodigal -d GCF_000270185.1_ASM27018v1_genomic.fna/cds.fna -a GCF_000270185.1_ASM27018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:07,123] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:07,123] [INFO] Task started: HMMsearch
[2024-01-24 13:46:07,123] [INFO] Running command: hmmsearch --tblout GCF_000270185.1_ASM27018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/reference_markers.hmm GCF_000270185.1_ASM27018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:07,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:07,384] [INFO] Found 6/6 markers.
[2024-01-24 13:46:07,410] [INFO] Query marker FASTA was written to GCF_000270185.1_ASM27018v1_genomic.fna/markers.fasta
[2024-01-24 13:46:07,411] [INFO] Task started: Blastn
[2024-01-24 13:46:07,411] [INFO] Running command: blastn -query GCF_000270185.1_ASM27018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/reference_markers.fasta -out GCF_000270185.1_ASM27018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:08,137] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:08,140] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:08,141] [INFO] Target genome list was writen to GCF_000270185.1_ASM27018v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:08,211] [INFO] Task started: fastANI
[2024-01-24 13:46:08,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3b1832-1898-4ace-964c-a90a45c3cdea/GCF_000270185.1_ASM27018v1_genomic.fna.gz --refList GCF_000270185.1_ASM27018v1_genomic.fna/target_genomes.txt --output GCF_000270185.1_ASM27018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:19,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:19,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:19,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:19,182] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:19,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:19,183] [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
Melissococcus plutonius	strain=ATCC 35311	GCA_000270185.1	33970	33970	type	True	100.0	684	689	95	conclusive
Melissococcus plutonius	strain=DSM 29964	GCA_014202715.1	33970	33970	type	True	99.9917	671	689	95	conclusive
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	77.9524	80	689	95	below_threshold
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	77.93	69	689	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	77.5364	96	689	95	below_threshold
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	77.5201	98	689	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	77.2844	135	689	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.267	81	689	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	77.2516	103	689	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000407445.1	155617	155617	type	True	77.2247	135	689	95	below_threshold
Enterococcus ureilyticus	strain=LMG 26676	GCA_001730315.1	1131292	1131292	type	True	77.2203	106	689	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	77.1509	77	689	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	77.1326	106	689	95	below_threshold
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	76.9677	112	689	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	76.951	102	689	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	76.9435	96	689	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	76.8526	107	689	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	76.842	74	689	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	76.8309	87	689	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	76.7173	132	689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:19,185] [INFO] DFAST Taxonomy check result was written to GCF_000270185.1_ASM27018v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:19,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:19,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:19,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/checkm_data
[2024-01-24 13:46:19,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:19,211] [INFO] Task started: CheckM
[2024-01-24 13:46:19,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000270185.1_ASM27018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000270185.1_ASM27018v1_genomic.fna/checkm_input GCF_000270185.1_ASM27018v1_genomic.fna/checkm_result
[2024-01-24 13:46:38,906] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:38,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:38,921] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:38,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:38,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000270185.1_ASM27018v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:38,923] [INFO] Task started: Blastn
[2024-01-24 13:46:38,923] [INFO] Running command: blastn -query GCF_000270185.1_ASM27018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4db5a6d-25c5-4299-b431-f6d174528462/dqc_reference/reference_markers_gtdb.fasta -out GCF_000270185.1_ASM27018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:40,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:40,024] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:40,025] [INFO] Target genome list was writen to GCF_000270185.1_ASM27018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:40,047] [INFO] Task started: fastANI
[2024-01-24 13:46:40,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3b1832-1898-4ace-964c-a90a45c3cdea/GCF_000270185.1_ASM27018v1_genomic.fna.gz --refList GCF_000270185.1_ASM27018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000270185.1_ASM27018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:52,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:52,763] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:52,763] [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_000270185.1	s__Melissococcus plutonius	100.0	687	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Melissococcus	95.0	99.79	99.26	0.98	0.96	19	conclusive
GCF_002141365.1	s__Enterococcus sp002141365	78.1257	118	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998885.1	s__Vagococcus penaei	77.93	69	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001730305.1	s__Enterococcus termitis	77.5693	95	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002148425.1	s__Enterococcus sp002148425	77.5547	113	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCA_001465115.1	s__Enterococcus silesiacus	77.5409	103	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000407145.1	s__Enterococcus caccae	77.4841	114	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002140715.1	s__Enterococcus sp002140715	77.4822	130	689	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	77.3896	103	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014397115.1	s__Vagococcus carniphilus	77.3526	79	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.3178	73	689	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_001730315.1	s__Enterococcus ureilyticus	77.2203	106	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_000407445.1	s__Enterococcus moraviensis	77.2132	135	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.173	81	689	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_000407285.1	s__Enterococcus_F saccharolyticus	77.1509	77	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001730295.1	s__Enterococcus plantarum	77.1326	106	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.1006	77	689	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_017315945.1	s__Enterococcus_B sp017315945	77.0937	91	689	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_001742285.1	s__Enterococcus rivorum	76.9907	111	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007990225.1	s__Enterococcus_B villorum	76.951	102	689	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_001886195.1	s__Enterococcus_B ratti	76.8935	98	689	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_019218635.1	s__Enterococcus_A sp019218635	76.8309	87	689	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_001885735.1	s__Enterococcus_C canintestini	76.7815	80	689	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:52,770] [INFO] GTDB search result was written to GCF_000270185.1_ASM27018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:52,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:52,777] [INFO] DFAST_QC result json was written to GCF_000270185.1_ASM27018v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:52,777] [INFO] DFAST_QC completed!
[2024-01-24 13:46:52,777] [INFO] Total running time: 0h0m51s