[2024-01-24 13:17:13,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,874] [INFO] DQC Reference Directory: /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference
[2024-01-24 13:17:15,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,236] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ee11062-67c6-473b-be7f-dddf048b24d5/GCF_003355475.1_ASM335547v1_genomic.fna.gz | prodigal -d GCF_003355475.1_ASM335547v1_genomic.fna/cds.fna -a GCF_003355475.1_ASM335547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:26,028] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:26,028] [INFO] Task started: HMMsearch
[2024-01-24 13:17:26,029] [INFO] Running command: hmmsearch --tblout GCF_003355475.1_ASM335547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/reference_markers.hmm GCF_003355475.1_ASM335547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:26,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:26,324] [INFO] Found 6/6 markers.
[2024-01-24 13:17:26,364] [INFO] Query marker FASTA was written to GCF_003355475.1_ASM335547v1_genomic.fna/markers.fasta
[2024-01-24 13:17:26,364] [INFO] Task started: Blastn
[2024-01-24 13:17:26,364] [INFO] Running command: blastn -query GCF_003355475.1_ASM335547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/reference_markers.fasta -out GCF_003355475.1_ASM335547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:27,645] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:27,649] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:27,649] [INFO] Target genome list was writen to GCF_003355475.1_ASM335547v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:27,670] [INFO] Task started: fastANI
[2024-01-24 13:17:27,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ee11062-67c6-473b-be7f-dddf048b24d5/GCF_003355475.1_ASM335547v1_genomic.fna.gz --refList GCF_003355475.1_ASM335547v1_genomic.fna/target_genomes.txt --output GCF_003355475.1_ASM335547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:41,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:41,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:41,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:41,081] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:41,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:41,081] [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 saurashtrense	strain=DSM 23186	GCA_003355475.1	556288	556288	type	True	100.0	1239	1240	95	conclusive
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	99.9812	1221	1240	95	conclusive
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	85.6918	888	1240	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	85.0808	901	1240	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	84.9117	810	1240	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	84.8863	847	1240	95	below_threshold
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	84.8288	883	1240	95	below_threshold
Brachybacterium avium	strain=VR2415	GCA_002216795.1	2017485	2017485	type	True	84.4812	840	1240	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	82.1666	656	1240	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	80.6922	668	1240	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	80.5456	685	1240	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.8678	334	1240	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.8629	332	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:41,083] [INFO] DFAST Taxonomy check result was written to GCF_003355475.1_ASM335547v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:41,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:41,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:41,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/checkm_data
[2024-01-24 13:17:41,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:41,128] [INFO] Task started: CheckM
[2024-01-24 13:17:41,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003355475.1_ASM335547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003355475.1_ASM335547v1_genomic.fna/checkm_input GCF_003355475.1_ASM335547v1_genomic.fna/checkm_result
[2024-01-24 13:19:07,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:07,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:07,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:07,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003355475.1_ASM335547v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:07,236] [INFO] Task started: Blastn
[2024-01-24 13:19:07,236] [INFO] Running command: blastn -query GCF_003355475.1_ASM335547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge45a92fe-0c42-447f-a13d-ceeeb2c54a7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003355475.1_ASM335547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:09,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:09,203] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:09,204] [INFO] Target genome list was writen to GCF_003355475.1_ASM335547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:09,214] [INFO] Task started: fastANI
[2024-01-24 13:19:09,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ee11062-67c6-473b-be7f-dddf048b24d5/GCF_003355475.1_ASM335547v1_genomic.fna.gz --refList GCF_003355475.1_ASM335547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003355475.1_ASM335547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:19,207] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,221] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:19,221] [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_003355475.1	s__Brachybacterium saurashtrense	100.0	1240	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_000023405.1	s__Brachybacterium faecium	85.7142	886	1240	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	85.4855	890	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	96.80	96.03	0.88	0.86	7	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	85.0837	901	1240	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	85.0774	909	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.17	99.17	0.95	0.95	2	-
GCF_002407185.1	s__Brachybacterium vulturis	84.9258	846	1240	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	84.8905	878	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204755.1	s__Brachybacterium aquaticum	84.8791	812	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216795.1	s__Brachybacterium avium	84.4795	841	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347015.1	s__Brachybacterium sp003347015	83.6079	858	1240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,224] [INFO] GTDB search result was written to GCF_003355475.1_ASM335547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:19,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:19,230] [INFO] DFAST_QC result json was written to GCF_003355475.1_ASM335547v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:19,230] [INFO] DFAST_QC completed!
[2024-01-24 13:19:19,230] [INFO] Total running time: 0h2m5s