[2024-01-24 13:45:58,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference
[2024-01-24 13:46:00,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,281] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eb5e492-83ac-4d92-aba0-b2d3c4919102/GCF_000426445.1_ASM42644v1_genomic.fna.gz | prodigal -d GCF_000426445.1_ASM42644v1_genomic.fna/cds.fna -a GCF_000426445.1_ASM42644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:12,610] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:12,611] [INFO] Task started: HMMsearch
[2024-01-24 13:46:12,611] [INFO] Running command: hmmsearch --tblout GCF_000426445.1_ASM42644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/reference_markers.hmm GCF_000426445.1_ASM42644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,891] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,931] [INFO] Query marker FASTA was written to GCF_000426445.1_ASM42644v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,931] [INFO] Task started: Blastn
[2024-01-24 13:46:12,932] [INFO] Running command: blastn -query GCF_000426445.1_ASM42644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/reference_markers.fasta -out GCF_000426445.1_ASM42644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:14,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:14,087] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:14,088] [INFO] Target genome list was writen to GCF_000426445.1_ASM42644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:14,116] [INFO] Task started: fastANI
[2024-01-24 13:46:14,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb5e492-83ac-4d92-aba0-b2d3c4919102/GCF_000426445.1_ASM42644v1_genomic.fna.gz --refList GCF_000426445.1_ASM42644v1_genomic.fna/target_genomes.txt --output GCF_000426445.1_ASM42644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:23,261] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:23,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:23,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:23,274] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:23,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:23,274] [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
Brevibacterium album	strain=DSM 18261	GCA_000426445.1	417948	417948	type	True	100.0	1356	1357	95	conclusive
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	80.3195	594	1357	95	below_threshold
Brevibacterium jeotgali	strain=SJ5-8	GCA_900169175.1	1262550	1262550	type	True	79.3519	512	1357	95	below_threshold
Brevibacterium jeotgali	strain=DSM 29217	GCA_007828155.1	1262550	1262550	type	True	79.318	513	1357	95	below_threshold
Brevibacterium yomogidense	strain=DSM 24850	GCA_016107685.1	946573	946573	type	True	79.3085	582	1357	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	79.2114	452	1357	95	below_threshold
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	79.024	479	1357	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	78.509	380	1357	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	77.6055	301	1357	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	77.4105	166	1357	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	77.2749	271	1357	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.6771	253	1357	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.6606	174	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:23,276] [INFO] DFAST Taxonomy check result was written to GCF_000426445.1_ASM42644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:23,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:23,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:23,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/checkm_data
[2024-01-24 13:46:23,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:23,321] [INFO] Task started: CheckM
[2024-01-24 13:46:23,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426445.1_ASM42644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426445.1_ASM42644v1_genomic.fna/checkm_input GCF_000426445.1_ASM42644v1_genomic.fna/checkm_result
[2024-01-24 13:47:31,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:31,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:31,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:31,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:31,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426445.1_ASM42644v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:31,955] [INFO] Task started: Blastn
[2024-01-24 13:47:31,955] [INFO] Running command: blastn -query GCF_000426445.1_ASM42644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f929f0-d092-4624-845f-366b02dd09ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426445.1_ASM42644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:33,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:33,700] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:33,700] [INFO] Target genome list was writen to GCF_000426445.1_ASM42644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:33,714] [INFO] Task started: fastANI
[2024-01-24 13:47:33,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb5e492-83ac-4d92-aba0-b2d3c4919102/GCF_000426445.1_ASM42644v1_genomic.fna.gz --refList GCF_000426445.1_ASM42644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426445.1_ASM42644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:41,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,137] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:41,137] [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_000426445.1	s__Brevibacterium album	100.0	1356	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019117325.1	s__Brevibacterium intestinigallinarum	80.4229	434	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285835.1	s__Brevibacterium senegalense	80.3391	592	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900163715.1	s__Brevibacterium yomogidense_A	79.6711	545	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.08	97.08	0.87	0.87	2	-
GCF_900169175.1	s__Brevibacterium jeotgali	79.3404	514	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005280295.1	s__Brevibacterium sp005280295	79.3112	467	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107685.1	s__Brevibacterium yomogidense	79.3021	581	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857845.1	s__Brevibacterium rongguiense	79.2496	449	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184225.1	s__Brevibacterium ihuae	79.063	475	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667225.1	s__Kocuria rhizophila	77.3573	169	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:41,144] [INFO] GTDB search result was written to GCF_000426445.1_ASM42644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:41,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:41,148] [INFO] DFAST_QC result json was written to GCF_000426445.1_ASM42644v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:41,148] [INFO] DFAST_QC completed!
[2024-01-24 13:47:41,148] [INFO] Total running time: 0h1m42s