[2024-01-25 20:12:35,769] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:35,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:35,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference
[2024-01-25 20:12:36,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:36,955] [INFO] Task started: Prodigal
[2024-01-25 20:12:36,955] [INFO] Running command: gunzip -c /var/lib/cwl/stge07d48cf-642b-4244-bc9a-e483ffb2ecb0/GCF_016907455.1_ASM1690745v1_genomic.fna.gz | prodigal -d GCF_016907455.1_ASM1690745v1_genomic.fna/cds.fna -a GCF_016907455.1_ASM1690745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:47,268] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:47,268] [INFO] Task started: HMMsearch
[2024-01-25 20:12:47,268] [INFO] Running command: hmmsearch --tblout GCF_016907455.1_ASM1690745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/reference_markers.hmm GCF_016907455.1_ASM1690745v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:47,474] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:47,475] [INFO] Found 6/6 markers.
[2024-01-25 20:12:47,503] [INFO] Query marker FASTA was written to GCF_016907455.1_ASM1690745v1_genomic.fna/markers.fasta
[2024-01-25 20:12:47,504] [INFO] Task started: Blastn
[2024-01-25 20:12:47,504] [INFO] Running command: blastn -query GCF_016907455.1_ASM1690745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/reference_markers.fasta -out GCF_016907455.1_ASM1690745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:48,649] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:48,652] [INFO] Selected 14 target genomes.
[2024-01-25 20:12:48,652] [INFO] Target genome list was writen to GCF_016907455.1_ASM1690745v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:48,666] [INFO] Task started: fastANI
[2024-01-25 20:12:48,667] [INFO] Running command: fastANI --query /var/lib/cwl/stge07d48cf-642b-4244-bc9a-e483ffb2ecb0/GCF_016907455.1_ASM1690745v1_genomic.fna.gz --refList GCF_016907455.1_ASM1690745v1_genomic.fna/target_genomes.txt --output GCF_016907455.1_ASM1690745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:07,512] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:07,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:07,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:07,522] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:07,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:07,523] [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 muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	100.0	1213	1215	95	conclusive
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	88.4658	846	1215	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	82.2985	642	1215	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	82.279	692	1215	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003355475.1	556288	556288	type	True	81.9759	720	1215	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	81.961	711	1215	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	81.5981	666	1215	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	81.3721	669	1215	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	81.344	670	1215	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	80.8048	507	1215	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	80.278	557	1215	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	80.2118	556	1215	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.9999	205	1215	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.736	259	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:07,528] [INFO] DFAST Taxonomy check result was written to GCF_016907455.1_ASM1690745v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:07,529] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:07,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:07,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/checkm_data
[2024-01-25 20:13:07,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:07,572] [INFO] Task started: CheckM
[2024-01-25 20:13:07,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907455.1_ASM1690745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907455.1_ASM1690745v1_genomic.fna/checkm_input GCF_016907455.1_ASM1690745v1_genomic.fna/checkm_result
[2024-01-25 20:14:19,165] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:19,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:19,190] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:19,190] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:19,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907455.1_ASM1690745v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:19,191] [INFO] Task started: Blastn
[2024-01-25 20:14:19,191] [INFO] Running command: blastn -query GCF_016907455.1_ASM1690745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14580067-fbbd-4c77-b747-1703ae94c427/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907455.1_ASM1690745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:21,044] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:21,047] [INFO] Selected 14 target genomes.
[2024-01-25 20:14:21,047] [INFO] Target genome list was writen to GCF_016907455.1_ASM1690745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:21,075] [INFO] Task started: fastANI
[2024-01-25 20:14:21,075] [INFO] Running command: fastANI --query /var/lib/cwl/stge07d48cf-642b-4244-bc9a-e483ffb2ecb0/GCF_016907455.1_ASM1690745v1_genomic.fna.gz --refList GCF_016907455.1_ASM1690745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907455.1_ASM1690745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:39,911] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:39,920] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:39,920] [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_016907455.1	s__Brachybacterium muris	100.0	1212	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	97.23	96.65	0.88	0.85	3	conclusive
GCF_015209585.1	s__Brachybacterium sp015209585	88.4469	849	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225825.1	s__Brachybacterium squillarum	82.3595	640	1215	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	82.3022	678	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	96.80	96.03	0.88	0.86	7	-
GCF_014204755.1	s__Brachybacterium aquaticum	82.2784	692	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184245.1	s__Brachybacterium massiliense	82.045	668	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355475.1	s__Brachybacterium saurashtrense	81.9971	717	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000023405.1	s__Brachybacterium faecium	81.6446	662	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407185.1	s__Brachybacterium vulturis	81.3739	668	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014400405.1	s__Brachybacterium sp014400405	81.2564	648	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	81.1107	608	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115335.1	s__Brachybacterium merdigallinarum	81.0006	468	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163655.1	s__Brachybacterium nesterenkovii	80.7952	508	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576425.1	s__Brachybacterium phenoliresistens	80.7837	590	1215	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 20:14:39,922] [INFO] GTDB search result was written to GCF_016907455.1_ASM1690745v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:39,922] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:39,925] [INFO] DFAST_QC result json was written to GCF_016907455.1_ASM1690745v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:39,926] [INFO] DFAST_QC completed!
[2024-01-25 20:14:39,926] [INFO] Total running time: 0h2m4s