[2024-01-24 12:14:48,396] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,398] [INFO] DQC Reference Directory: /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference
[2024-01-24 12:14:49,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,701] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg472f131b-dfb0-4e1b-8552-268b3c970cb9/GCF_016623465.1_ASM1662346v1_genomic.fna.gz | prodigal -d GCF_016623465.1_ASM1662346v1_genomic.fna/cds.fna -a GCF_016623465.1_ASM1662346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:00,018] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:00,018] [INFO] Task started: HMMsearch
[2024-01-24 12:15:00,018] [INFO] Running command: hmmsearch --tblout GCF_016623465.1_ASM1662346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/reference_markers.hmm GCF_016623465.1_ASM1662346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:00,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:00,234] [INFO] Found 6/6 markers.
[2024-01-24 12:15:00,264] [INFO] Query marker FASTA was written to GCF_016623465.1_ASM1662346v1_genomic.fna/markers.fasta
[2024-01-24 12:15:00,264] [INFO] Task started: Blastn
[2024-01-24 12:15:00,264] [INFO] Running command: blastn -query GCF_016623465.1_ASM1662346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/reference_markers.fasta -out GCF_016623465.1_ASM1662346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:01,415] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:01,418] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:01,419] [INFO] Target genome list was writen to GCF_016623465.1_ASM1662346v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:01,423] [INFO] Task started: fastANI
[2024-01-24 12:15:01,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg472f131b-dfb0-4e1b-8552-268b3c970cb9/GCF_016623465.1_ASM1662346v1_genomic.fna.gz --refList GCF_016623465.1_ASM1662346v1_genomic.fna/target_genomes.txt --output GCF_016623465.1_ASM1662346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:09,641] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:09,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:09,650] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:09,650] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:09,651] [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 halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	100.0	1256	1270	95	conclusive
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	96.8192	1136	1270	95	conclusive
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	94.5214	1131	1270	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	93.1456	1105	1270	95	below_threshold
Brachybacterium endophyticum	strain=M1HQ-2	GCA_003130585.1	2182385	2182385	type	True	84.8617	898	1270	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	81.0669	612	1270	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	80.0775	496	1270	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.0763	268	1270	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.9522	320	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,652] [INFO] DFAST Taxonomy check result was written to GCF_016623465.1_ASM1662346v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:09,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:09,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:09,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/checkm_data
[2024-01-24 12:15:09,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:09,692] [INFO] Task started: CheckM
[2024-01-24 12:15:09,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016623465.1_ASM1662346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016623465.1_ASM1662346v1_genomic.fna/checkm_input GCF_016623465.1_ASM1662346v1_genomic.fna/checkm_result
[2024-01-24 12:15:53,497] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:53,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:53,518] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:53,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:53,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016623465.1_ASM1662346v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:53,519] [INFO] Task started: Blastn
[2024-01-24 12:15:53,519] [INFO] Running command: blastn -query GCF_016623465.1_ASM1662346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge166184f-aa6b-4cf2-af19-bf669de0907e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016623465.1_ASM1662346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:55,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:55,383] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:55,383] [INFO] Target genome list was writen to GCF_016623465.1_ASM1662346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:55,391] [INFO] Task started: fastANI
[2024-01-24 12:15:55,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg472f131b-dfb0-4e1b-8552-268b3c970cb9/GCF_016623465.1_ASM1662346v1_genomic.fna.gz --refList GCF_016623465.1_ASM1662346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016623465.1_ASM1662346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:05,334] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:05,348] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:05,348] [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_016623465.1	s__Brachybacterium halotolerans	100.0	1260	1270	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_009299795.1	s__Brachybacterium subflavum	93.1456	1105	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130585.1	s__Brachybacterium endophyticum	84.8641	898	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490785.1	s__Brachybacterium sp005490785	81.5018	710	1270	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	81.205	655	1270	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	81.0707	612	1270	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	81.0361	615	1270	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	81.0118	690	1270	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	80.8088	539	1270	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	80.5558	663	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	80.5327	689	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209585.1	s__Brachybacterium sp015209585	80.0685	496	1270	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 12:16:05,350] [INFO] GTDB search result was written to GCF_016623465.1_ASM1662346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:05,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:05,355] [INFO] DFAST_QC result json was written to GCF_016623465.1_ASM1662346v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:05,356] [INFO] DFAST_QC completed!
[2024-01-24 12:16:05,356] [INFO] Total running time: 0h1m17s