[2024-01-24 11:26:38,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference
[2024-01-24 11:26:40,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,274] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg8267f95b-9a96-4be7-a57b-611dcab3ee90/GCF_014204755.1_ASM1420475v1_genomic.fna.gz | prodigal -d GCF_014204755.1_ASM1420475v1_genomic.fna/cds.fna -a GCF_014204755.1_ASM1420475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:49,869] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:49,870] [INFO] Task started: HMMsearch
[2024-01-24 11:26:49,870] [INFO] Running command: hmmsearch --tblout GCF_014204755.1_ASM1420475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/reference_markers.hmm GCF_014204755.1_ASM1420475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:50,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:50,128] [INFO] Found 6/6 markers.
[2024-01-24 11:26:50,156] [INFO] Query marker FASTA was written to GCF_014204755.1_ASM1420475v1_genomic.fna/markers.fasta
[2024-01-24 11:26:50,156] [INFO] Task started: Blastn
[2024-01-24 11:26:50,156] [INFO] Running command: blastn -query GCF_014204755.1_ASM1420475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/reference_markers.fasta -out GCF_014204755.1_ASM1420475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:51,408] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:51,411] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:51,412] [INFO] Target genome list was writen to GCF_014204755.1_ASM1420475v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:51,434] [INFO] Task started: fastANI
[2024-01-24 11:26:51,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg8267f95b-9a96-4be7-a57b-611dcab3ee90/GCF_014204755.1_ASM1420475v1_genomic.fna.gz --refList GCF_014204755.1_ASM1420475v1_genomic.fna/target_genomes.txt --output GCF_014204755.1_ASM1420475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:02,869] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:02,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:02,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:02,886] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:02,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:02,887] [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 aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	100.0	1149	1149	95	conclusive
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003355475.1	556288	556288	type	True	84.7657	821	1149	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	84.7021	814	1149	95	below_threshold
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	84.5707	804	1149	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	84.5418	792	1149	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	84.1162	818	1149	95	below_threshold
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	83.7756	763	1149	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	83.2594	690	1149	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	82.0203	653	1149	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	81.4456	642	1149	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	81.4026	616	1149	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.4982	344	1149	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.8114	250	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:02,888] [INFO] DFAST Taxonomy check result was written to GCF_014204755.1_ASM1420475v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:02,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:02,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:02,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/checkm_data
[2024-01-24 11:27:02,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:02,924] [INFO] Task started: CheckM
[2024-01-24 11:27:02,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204755.1_ASM1420475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204755.1_ASM1420475v1_genomic.fna/checkm_input GCF_014204755.1_ASM1420475v1_genomic.fna/checkm_result
[2024-01-24 11:28:00,932] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:00,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:00,956] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:00,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:00,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204755.1_ASM1420475v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:00,957] [INFO] Task started: Blastn
[2024-01-24 11:28:00,958] [INFO] Running command: blastn -query GCF_014204755.1_ASM1420475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b3af87-f0a9-41c5-a552-6f1b557cc5ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204755.1_ASM1420475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:02,994] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:02,999] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:02,999] [INFO] Target genome list was writen to GCF_014204755.1_ASM1420475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:03,009] [INFO] Task started: fastANI
[2024-01-24 11:28:03,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg8267f95b-9a96-4be7-a57b-611dcab3ee90/GCF_014204755.1_ASM1420475v1_genomic.fna.gz --refList GCF_014204755.1_ASM1420475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204755.1_ASM1420475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:12,270] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:12,284] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:12,284] [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_014204755.1	s__Brachybacterium aquaticum	100.0	1149	1149	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_003994255.1	s__Brachybacterium paraconglomeratum	86.5771	893	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	96.80	96.03	0.88	0.86	7	-
GCF_003711805.1	s__Brachybacterium intestinipullorum	85.6423	859	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.17	99.17	0.95	0.95	2	-
GCF_003355475.1	s__Brachybacterium saurashtrense	84.7787	819	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900184245.1	s__Brachybacterium massiliense	84.6146	801	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023405.1	s__Brachybacterium faecium	84.5542	791	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	84.1109	818	1149	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	83.4431	742	1149	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	83.263	690	1149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118275.1	s__Brachybacterium merdavium	81.3096	636	1149	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 11:28:12,286] [INFO] GTDB search result was written to GCF_014204755.1_ASM1420475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:12,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:12,290] [INFO] DFAST_QC result json was written to GCF_014204755.1_ASM1420475v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:12,290] [INFO] DFAST_QC completed!
[2024-01-24 11:28:12,290] [INFO] Total running time: 0h1m33s