[2024-01-24 13:08:58,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference
[2024-01-24 13:08:59,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,674] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg0db22487-8b08-4d67-bf87-a7833c5a71b0/GCF_000178455.1_ASM17845v1_genomic.fna.gz | prodigal -d GCF_000178455.1_ASM17845v1_genomic.fna/cds.fna -a GCF_000178455.1_ASM17845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:07,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:07,742] [INFO] Task started: HMMsearch
[2024-01-24 13:09:07,742] [INFO] Running command: hmmsearch --tblout GCF_000178455.1_ASM17845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/reference_markers.hmm GCF_000178455.1_ASM17845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:07,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:07,972] [INFO] Found 6/6 markers.
[2024-01-24 13:09:08,000] [INFO] Query marker FASTA was written to GCF_000178455.1_ASM17845v1_genomic.fna/markers.fasta
[2024-01-24 13:09:08,001] [INFO] Task started: Blastn
[2024-01-24 13:09:08,001] [INFO] Running command: blastn -query GCF_000178455.1_ASM17845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/reference_markers.fasta -out GCF_000178455.1_ASM17845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:08,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:08,665] [INFO] Selected 23 target genomes.
[2024-01-24 13:09:08,665] [INFO] Target genome list was writen to GCF_000178455.1_ASM17845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:08,710] [INFO] Task started: fastANI
[2024-01-24 13:09:08,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg0db22487-8b08-4d67-bf87-a7833c5a71b0/GCF_000178455.1_ASM17845v1_genomic.fna.gz --refList GCF_000178455.1_ASM17845v1_genomic.fna/target_genomes.txt --output GCF_000178455.1_ASM17845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:23,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:23,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:23,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:24,012] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:24,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:24,012] [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 mcbrellneri	strain=ATCC 49030	GCA_000178455.1	53363	53363	type	True	100.0	803	808	95	conclusive
Brevibacterium paucivorans	strain=DSM 13657	GCA_016907735.1	170994	170994	type	True	88.2072	683	808	95	below_threshold
Brevibacterium ravenspurgense	strain=CCUG56047	GCA_001584615.1	479117	479117	type	True	78.2366	127	808	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	77.0385	86	808	95	below_threshold
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	77.0105	97	808	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	76.9864	96	808	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	76.9565	84	808	95	below_threshold
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	76.9114	79	808	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	76.9096	72	808	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	76.885	72	808	95	below_threshold
Brevibacterium yomogidense	strain=DSM 24850	GCA_016107685.1	946573	946573	type	True	76.6232	68	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:24,014] [INFO] DFAST Taxonomy check result was written to GCF_000178455.1_ASM17845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:24,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:24,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:24,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/checkm_data
[2024-01-24 13:09:24,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:24,044] [INFO] Task started: CheckM
[2024-01-24 13:09:24,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178455.1_ASM17845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178455.1_ASM17845v1_genomic.fna/checkm_input GCF_000178455.1_ASM17845v1_genomic.fna/checkm_result
[2024-01-24 13:09:52,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:52,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:52,803] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:52,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:52,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178455.1_ASM17845v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:52,804] [INFO] Task started: Blastn
[2024-01-24 13:09:52,804] [INFO] Running command: blastn -query GCF_000178455.1_ASM17845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47716d00-736e-431c-8d67-a4f14e3ddba5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178455.1_ASM17845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:53,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:53,691] [INFO] Selected 19 target genomes.
[2024-01-24 13:09:53,691] [INFO] Target genome list was writen to GCF_000178455.1_ASM17845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:53,851] [INFO] Task started: fastANI
[2024-01-24 13:09:53,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg0db22487-8b08-4d67-bf87-a7833c5a71b0/GCF_000178455.1_ASM17845v1_genomic.fna.gz --refList GCF_000178455.1_ASM17845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000178455.1_ASM17845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:04,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:04,242] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:04,242] [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_000178455.1	s__Brevibacterium mcbrellneri	100.0	803	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907735.1	s__Brevibacterium paucivorans	88.2072	683	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815905.1	s__Brevibacterium sp001815905	79.0353	114	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.85	98.78	0.94	0.92	3	-
GCF_001584615.1	s__Brevibacterium ravenspurgense	78.2366	127	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.93	96.42	0.92	0.90	8	-
GCF_900169265.1	s__Brevibacterium iodinum	77.3073	69	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013359525.1	s__Brevibacterium luteolum_A	77.0592	87	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	-
GCF_013280495.1	s__Brevibacterium permense	76.9565	84	808	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	76.9114	79	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013623905.1	s__Brevibacterium sediminis	76.9096	72	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_018137945.1	s__Brevibacterium sp018137945	76.8844	63	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.80	97.80	0.94	0.94	2	-
GCF_006489205.1	s__Brevibacterium sp006489205	76.8622	68	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.50	98.50	0.93	0.93	2	-
GCA_019117325.1	s__Brevibacterium intestinigallinarum	76.7194	52	808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:04,244] [INFO] GTDB search result was written to GCF_000178455.1_ASM17845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:04,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:04,248] [INFO] DFAST_QC result json was written to GCF_000178455.1_ASM17845v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:04,249] [INFO] DFAST_QC completed!
[2024-01-24 13:10:04,249] [INFO] Total running time: 0h1m6s