[2024-01-24 15:19:50,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:50,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:50,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference
[2024-01-24 15:19:51,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:51,512] [INFO] Task started: Prodigal
[2024-01-24 15:19:51,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c40f45-896c-4615-bcd4-a6aa7becf926/GCF_014397115.1_ASM1439711v1_genomic.fna.gz | prodigal -d GCF_014397115.1_ASM1439711v1_genomic.fna/cds.fna -a GCF_014397115.1_ASM1439711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:57,024] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:57,024] [INFO] Task started: HMMsearch
[2024-01-24 15:19:57,024] [INFO] Running command: hmmsearch --tblout GCF_014397115.1_ASM1439711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/reference_markers.hmm GCF_014397115.1_ASM1439711v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:57,325] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:57,327] [INFO] Found 6/6 markers.
[2024-01-24 15:19:57,358] [INFO] Query marker FASTA was written to GCF_014397115.1_ASM1439711v1_genomic.fna/markers.fasta
[2024-01-24 15:19:57,359] [INFO] Task started: Blastn
[2024-01-24 15:19:57,359] [INFO] Running command: blastn -query GCF_014397115.1_ASM1439711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/reference_markers.fasta -out GCF_014397115.1_ASM1439711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:58,024] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:58,027] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:58,028] [INFO] Target genome list was writen to GCF_014397115.1_ASM1439711v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:58,040] [INFO] Task started: fastANI
[2024-01-24 15:19:58,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c40f45-896c-4615-bcd4-a6aa7becf926/GCF_014397115.1_ASM1439711v1_genomic.fna.gz --refList GCF_014397115.1_ASM1439711v1_genomic.fna/target_genomes.txt --output GCF_014397115.1_ASM1439711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:06,759] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:06,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:06,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:06,775] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:06,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:06,775] [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 carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	100.0	1037	1041	95	conclusive
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	80.372	411	1041	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	80.2381	419	1041	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	80.232	464	1041	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	79.686	94	1041	95	below_threshold
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	79.4885	212	1041	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	79.48	214	1041	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	79.3805	74	1041	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	79.0564	241	1041	95	below_threshold
Carnobacterium funditum	strain=pf3	GCA_000744185.1	2752	2752	type	True	78.7969	71	1041	95	below_threshold
Vagococcus silagei	strain=2B-2	GCA_004795745.1	2508885	2508885	type	True	78.6956	216	1041	95	below_threshold
Enterococcus wangshanyuanii	strain=CGMCC 1.15942	GCA_014644255.1	2005703	2005703	type	True	77.8099	70	1041	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.6937	88	1041	95	below_threshold
Melissococcus plutonius	strain=ATCC 35311	GCA_000270185.1	33970	33970	type	True	77.6883	85	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:06,777] [INFO] DFAST Taxonomy check result was written to GCF_014397115.1_ASM1439711v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:06,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:06,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:06,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/checkm_data
[2024-01-24 15:20:06,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:06,810] [INFO] Task started: CheckM
[2024-01-24 15:20:06,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014397115.1_ASM1439711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014397115.1_ASM1439711v1_genomic.fna/checkm_input GCF_014397115.1_ASM1439711v1_genomic.fna/checkm_result
[2024-01-24 15:20:30,360] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:30,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:30,385] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:30,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:30,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014397115.1_ASM1439711v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:30,386] [INFO] Task started: Blastn
[2024-01-24 15:20:30,386] [INFO] Running command: blastn -query GCF_014397115.1_ASM1439711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2774c755-3ee2-44f4-ab6d-e3f92599c6f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014397115.1_ASM1439711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:31,191] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:31,195] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:31,195] [INFO] Target genome list was writen to GCF_014397115.1_ASM1439711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:31,203] [INFO] Task started: fastANI
[2024-01-24 15:20:31,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c40f45-896c-4615-bcd4-a6aa7becf926/GCF_014397115.1_ASM1439711v1_genomic.fna.gz --refList GCF_014397115.1_ASM1439711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014397115.1_ASM1439711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:36,628] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:36,641] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:36,641] [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_014397115.1	s__Vagococcus carniphilus	100.0	1037	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900163795.1	s__Vagococcus fluvialis_A	80.2703	452	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011304195.1	s__Vagococcus hydrophili	80.2554	467	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337315.1	s__Vagococcus fluvialis	80.246	418	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_017316185.1	s__Vagococcus sp017316185	80.1816	349	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870205.1	s__Vagococcus teuberi	79.5117	211	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_002026305.1	s__Vagococcus martis	79.4744	213	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
GCF_003950315.1	s__Vagococcus bubulae	79.0527	243	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795745.1	s__Vagococcus silagei	78.6664	217	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003462485.1	s__Vagococcus sp003462485	78.4287	223	1041	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:36,643] [INFO] GTDB search result was written to GCF_014397115.1_ASM1439711v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:36,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:36,647] [INFO] DFAST_QC result json was written to GCF_014397115.1_ASM1439711v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:36,647] [INFO] DFAST_QC completed!
[2024-01-24 15:20:36,647] [INFO] Total running time: 0h0m46s