[2024-01-25 17:39:35,424] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference
[2024-01-25 17:39:36,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,620] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg29dca51f-6e81-45b3-b03c-76f1f840202d/GCF_017876515.1_ASM1787651v1_genomic.fna.gz | prodigal -d GCF_017876515.1_ASM1787651v1_genomic.fna/cds.fna -a GCF_017876515.1_ASM1787651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:48,216] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:48,217] [INFO] Task started: HMMsearch
[2024-01-25 17:39:48,217] [INFO] Running command: hmmsearch --tblout GCF_017876515.1_ASM1787651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/reference_markers.hmm GCF_017876515.1_ASM1787651v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:48,482] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:48,484] [INFO] Found 6/6 markers.
[2024-01-25 17:39:48,524] [INFO] Query marker FASTA was written to GCF_017876515.1_ASM1787651v1_genomic.fna/markers.fasta
[2024-01-25 17:39:48,525] [INFO] Task started: Blastn
[2024-01-25 17:39:48,525] [INFO] Running command: blastn -query GCF_017876515.1_ASM1787651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/reference_markers.fasta -out GCF_017876515.1_ASM1787651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:49,644] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:49,646] [INFO] Selected 15 target genomes.
[2024-01-25 17:39:49,647] [INFO] Target genome list was writen to GCF_017876515.1_ASM1787651v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:49,663] [INFO] Task started: fastANI
[2024-01-25 17:39:49,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg29dca51f-6e81-45b3-b03c-76f1f840202d/GCF_017876515.1_ASM1787651v1_genomic.fna.gz --refList GCF_017876515.1_ASM1787651v1_genomic.fna/target_genomes.txt --output GCF_017876515.1_ASM1787651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:05,242] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:05,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:05,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:05,253] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:05,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:05,254] [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
Brachybacterium fresconis	strain=DSM 14564	GCA_017876515.1	173363	173363	type	True	100.0	1542	1542	95	conclusive
Brachybacterium sacelli	strain=DSM 14566	GCA_017876545.1	173364	173364	type	True	87.0345	1142	1542	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	83.3263	893	1542	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	83.22	880	1542	95	below_threshold
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	83.1453	849	1542	95	below_threshold
Brachybacterium avium	strain=VR2415	GCA_002216795.1	2017485	2017485	type	True	83.084	848	1542	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	82.9395	922	1542	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	82.8143	795	1542	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	82.7322	877	1542	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	82.2831	726	1542	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	81.3064	654	1542	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	80.5694	691	1542	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	80.5126	707	1542	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.7294	318	1542	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.6333	312	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:05,255] [INFO] DFAST Taxonomy check result was written to GCF_017876515.1_ASM1787651v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:05,256] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:05,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:05,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/checkm_data
[2024-01-25 17:40:05,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:05,301] [INFO] Task started: CheckM
[2024-01-25 17:40:05,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876515.1_ASM1787651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876515.1_ASM1787651v1_genomic.fna/checkm_input GCF_017876515.1_ASM1787651v1_genomic.fna/checkm_result
[2024-01-25 17:41:51,300] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:51,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:51,321] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:51,321] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:51,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876515.1_ASM1787651v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:51,322] [INFO] Task started: Blastn
[2024-01-25 17:41:51,322] [INFO] Running command: blastn -query GCF_017876515.1_ASM1787651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf379fb9e-1969-45ca-a9fb-1587f39d6d7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876515.1_ASM1787651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:53,200] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:53,204] [INFO] Selected 11 target genomes.
[2024-01-25 17:41:53,204] [INFO] Target genome list was writen to GCF_017876515.1_ASM1787651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:53,221] [INFO] Task started: fastANI
[2024-01-25 17:41:53,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg29dca51f-6e81-45b3-b03c-76f1f840202d/GCF_017876515.1_ASM1787651v1_genomic.fna.gz --refList GCF_017876515.1_ASM1787651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876515.1_ASM1787651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:05,615] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:05,623] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:05,623] [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_017876515.1	s__Brachybacterium fresconis	100.0	1541	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001969445.1	s__Brachybacterium sp001969445	91.4382	1208	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876545.1	s__Brachybacterium sacelli	87.0282	1142	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014897585.1	s__Brachybacterium tyrofermentans	83.7946	1010	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	97.83	97.83	0.89	0.89	2	-
GCF_014897705.1	s__Brachybacterium sp014897705	83.6444	1050	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002332425.1	s__Brachybacterium alimentarium	83.5212	987	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.24	99.17	0.94	0.92	9	-
GCF_000023405.1	s__Brachybacterium faecium	83.2969	892	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994255.1	s__Brachybacterium paraconglomeratum	83.2544	873	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	96.80	96.03	0.88	0.86	7	-
GCF_002407185.1	s__Brachybacterium vulturis	83.215	877	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711805.1	s__Brachybacterium intestinipullorum	82.958	915	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.17	99.17	0.95	0.95	2	-
GCF_003347015.1	s__Brachybacterium sp003347015	82.8969	872	1542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:05,624] [INFO] GTDB search result was written to GCF_017876515.1_ASM1787651v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:05,625] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:05,638] [INFO] DFAST_QC result json was written to GCF_017876515.1_ASM1787651v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:05,638] [INFO] DFAST_QC completed!
[2024-01-25 17:42:05,638] [INFO] Total running time: 0h2m30s