[2024-01-25 18:55:20,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:20,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:20,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference
[2024-01-25 18:55:21,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:21,648] [INFO] Task started: Prodigal
[2024-01-25 18:55:21,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg0856ca14-0106-4b8a-ab4f-c5080a6d5da9/GCF_017829975.1_ASM1782997v1_genomic.fna.gz | prodigal -d GCF_017829975.1_ASM1782997v1_genomic.fna/cds.fna -a GCF_017829975.1_ASM1782997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:31,915] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:31,915] [INFO] Task started: HMMsearch
[2024-01-25 18:55:31,915] [INFO] Running command: hmmsearch --tblout GCF_017829975.1_ASM1782997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/reference_markers.hmm GCF_017829975.1_ASM1782997v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:32,188] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:32,189] [INFO] Found 6/6 markers.
[2024-01-25 18:55:32,232] [INFO] Query marker FASTA was written to GCF_017829975.1_ASM1782997v1_genomic.fna/markers.fasta
[2024-01-25 18:55:32,233] [INFO] Task started: Blastn
[2024-01-25 18:55:32,233] [INFO] Running command: blastn -query GCF_017829975.1_ASM1782997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/reference_markers.fasta -out GCF_017829975.1_ASM1782997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:32,782] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:32,786] [INFO] Selected 25 target genomes.
[2024-01-25 18:55:32,786] [INFO] Target genome list was writen to GCF_017829975.1_ASM1782997v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:32,799] [INFO] Task started: fastANI
[2024-01-25 18:55:32,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg0856ca14-0106-4b8a-ab4f-c5080a6d5da9/GCF_017829975.1_ASM1782997v1_genomic.fna.gz --refList GCF_017829975.1_ASM1782997v1_genomic.fna/target_genomes.txt --output GCF_017829975.1_ASM1782997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:45,296] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:45,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:45,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:45,307] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:45,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:45,308] [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 allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	100.0	1880	1883	95	conclusive
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	78.4006	211	1883	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.875	80	1883	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	77.6438	86	1883	95	below_threshold
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	77.6333	74	1883	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	77.6008	61	1883	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000407505.1	154621	154621	type	True	77.5595	72	1883	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	77.52	73	1883	95	below_threshold
Carnobacterium divergens	strain=66	GCA_000744255.1	2748	2748	type	True	77.4548	75	1883	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	77.3926	66	1883	95	below_threshold
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	77.3771	75	1883	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	77.3768	62	1883	95	below_threshold
Enterococcus phoeniculicola	strain=DSM 14726	GCA_001886115.1	154621	154621	type	True	77.3115	68	1883	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	77.2322	95	1883	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	77.2236	99	1883	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	77.1731	59	1883	95	below_threshold
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	77.0867	71	1883	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.0622	71	1883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:45,309] [INFO] DFAST Taxonomy check result was written to GCF_017829975.1_ASM1782997v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:45,309] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:45,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:45,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/checkm_data
[2024-01-25 18:55:45,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:45,365] [INFO] Task started: CheckM
[2024-01-25 18:55:45,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017829975.1_ASM1782997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017829975.1_ASM1782997v1_genomic.fna/checkm_input GCF_017829975.1_ASM1782997v1_genomic.fna/checkm_result
[2024-01-25 18:56:19,186] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:19,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:19,202] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:19,203] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:19,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017829975.1_ASM1782997v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:19,204] [INFO] Task started: Blastn
[2024-01-25 18:56:19,204] [INFO] Running command: blastn -query GCF_017829975.1_ASM1782997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c280b8-dc06-49ad-ba22-88008fbbd537/dqc_reference/reference_markers_gtdb.fasta -out GCF_017829975.1_ASM1782997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:19,983] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:19,992] [INFO] Selected 22 target genomes.
[2024-01-25 18:56:19,993] [INFO] Target genome list was writen to GCF_017829975.1_ASM1782997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:20,016] [INFO] Task started: fastANI
[2024-01-25 18:56:20,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg0856ca14-0106-4b8a-ab4f-c5080a6d5da9/GCF_017829975.1_ASM1782997v1_genomic.fna.gz --refList GCF_017829975.1_ASM1782997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017829975.1_ASM1782997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:34,175] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:34,186] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:34,187] [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_017829975.1	s__Vagococcus_D sp017829975	100.0	1880	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003987495.1	s__Vagococcus_D salmoninarum	78.399	211	1883	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_002813755.1	s__Enterococcus_B mundtii	78.1873	52	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCF_004795745.1	s__Vagococcus silagei	77.8934	63	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	77.8445	69	1883	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_000406925.1	s__Enterococcus_E columbae	77.8444	55	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	99.98	99.97	1.00	0.99	4	-
GCF_000633635.1	s__Enterococcus crotali	77.6438	86	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_000407505.1	s__Enterococcus_B phoeniculicola	77.5595	72	1883	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_001870205.1	s__Vagococcus teuberi	77.5428	73	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_003462485.1	s__Vagococcus sp003462485	77.5382	71	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001465115.1	s__Enterococcus silesiacus	77.4898	89	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000744255.1	s__Carnobacterium divergens	77.4548	75	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_003950315.1	s__Vagococcus bubulae	77.3926	66	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987595.1	s__Vagococcus_E entomophilus	77.374	67	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140715.1	s__Enterococcus sp002140715	77.3169	85	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011304195.1	s__Vagococcus hydrophili	77.2322	95	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.0482	59	1883	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_001885735.1	s__Enterococcus_C canintestini	76.6463	70	1883	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:34,192] [INFO] GTDB search result was written to GCF_017829975.1_ASM1782997v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:34,193] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:34,196] [INFO] DFAST_QC result json was written to GCF_017829975.1_ASM1782997v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:34,196] [INFO] DFAST_QC completed!
[2024-01-25 18:56:34,196] [INFO] Total running time: 0h1m14s