[2024-01-24 13:31:33,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference
[2024-01-24 13:31:34,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,647] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc4d405e-d5e1-40c1-a402-d8d3b978e7dc/GCF_021729135.1_ASM2172913v1_genomic.fna.gz | prodigal -d GCF_021729135.1_ASM2172913v1_genomic.fna/cds.fna -a GCF_021729135.1_ASM2172913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:45,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:45,354] [INFO] Task started: HMMsearch
[2024-01-24 13:31:45,354] [INFO] Running command: hmmsearch --tblout GCF_021729135.1_ASM2172913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/reference_markers.hmm GCF_021729135.1_ASM2172913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:45,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:45,626] [INFO] Found 6/6 markers.
[2024-01-24 13:31:45,661] [INFO] Query marker FASTA was written to GCF_021729135.1_ASM2172913v1_genomic.fna/markers.fasta
[2024-01-24 13:31:45,662] [INFO] Task started: Blastn
[2024-01-24 13:31:45,662] [INFO] Running command: blastn -query GCF_021729135.1_ASM2172913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/reference_markers.fasta -out GCF_021729135.1_ASM2172913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:46,922] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:46,926] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:46,927] [INFO] Target genome list was writen to GCF_021729135.1_ASM2172913v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:46,933] [INFO] Task started: fastANI
[2024-01-24 13:31:46,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc4d405e-d5e1-40c1-a402-d8d3b978e7dc/GCF_021729135.1_ASM2172913v1_genomic.fna.gz --refList GCF_021729135.1_ASM2172913v1_genomic.fna/target_genomes.txt --output GCF_021729135.1_ASM2172913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:01,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:01,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:01,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:01,409] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:01,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:01,410] [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 daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	100.0	1158	1162	95	conclusive
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	80.8087	589	1162	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	79.367	414	1162	95	below_threshold
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	79.328	420	1162	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	79.3154	444	1162	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	78.9368	401	1162	95	below_threshold
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	78.246	382	1162	95	below_threshold
Brevibacterium limosum	strain=o2	GCA_011617705.1	2697565	2697565	type	True	78.1978	320	1162	95	below_threshold
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	78.1383	341	1162	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_014639315.1	1774748	1774748	type	True	78.014	254	1162	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	78.0067	253	1162	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	77.6791	267	1162	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.487	196	1162	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	76.4276	198	1162	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	76.0263	203	1162	95	below_threshold
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	75.9751	202	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:01,411] [INFO] DFAST Taxonomy check result was written to GCF_021729135.1_ASM2172913v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:01,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:01,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:01,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/checkm_data
[2024-01-24 13:32:01,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:01,453] [INFO] Task started: CheckM
[2024-01-24 13:32:01,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021729135.1_ASM2172913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021729135.1_ASM2172913v1_genomic.fna/checkm_input GCF_021729135.1_ASM2172913v1_genomic.fna/checkm_result
[2024-01-24 13:32:54,571] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:54,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,589] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:54,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:54,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021729135.1_ASM2172913v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:54,591] [INFO] Task started: Blastn
[2024-01-24 13:32:54,591] [INFO] Running command: blastn -query GCF_021729135.1_ASM2172913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766b08f6-d083-4344-aa67-f8b8bf9c1a64/dqc_reference/reference_markers_gtdb.fasta -out GCF_021729135.1_ASM2172913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:56,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:56,655] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:56,655] [INFO] Target genome list was writen to GCF_021729135.1_ASM2172913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:56,668] [INFO] Task started: fastANI
[2024-01-24 13:32:56,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc4d405e-d5e1-40c1-a402-d8d3b978e7dc/GCF_021729135.1_ASM2172913v1_genomic.fna.gz --refList GCF_021729135.1_ASM2172913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021729135.1_ASM2172913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:08,270] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,282] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:33:08,282] [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_005280295.1	s__Brevibacterium sp005280295	80.9703	613	1162	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	80.8087	589	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359525.1	s__Brevibacterium luteolum_A	79.3622	448	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	-
GCF_013004595.1	s__Brevibacterium luteolum	79.3075	421	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	-
GCF_009857845.1	s__Brevibacterium rongguiense	78.9148	402	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315415.1	s__Brevibacterium celere_A	78.6345	382	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006489205.1	s__Brevibacterium sp006489205	78.5779	376	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.50	98.50	0.93	0.93	2	-
GCF_018137945.1	s__Brevibacterium sp018137945	78.5094	391	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.80	97.80	0.94	0.94	2	-
GCF_000285835.1	s__Brevibacterium senegalense	78.2427	382	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011617245.1	s__Brevibacterium sp011617245	78.1277	342	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639315.1	s__Sediminivirga luteola	78.014	254	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Sediminivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	76.3879	211	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000974985.2	s__Streptomyces mangrovisoli	76.0326	202	1162	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,286] [INFO] GTDB search result was written to GCF_021729135.1_ASM2172913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:08,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:08,290] [INFO] DFAST_QC result json was written to GCF_021729135.1_ASM2172913v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:08,290] [INFO] DFAST_QC completed!
[2024-01-24 13:33:08,290] [INFO] Total running time: 0h1m35s