[2024-01-24 13:13:46,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:46,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:46,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference
[2024-01-24 13:13:47,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:47,553] [INFO] Task started: Prodigal
[2024-01-24 13:13:47,554] [INFO] Running command: gunzip -c /var/lib/cwl/stga3575132-6197-4a43-9134-9375025ecab4/GCF_008868375.1_ASM886837v1_genomic.fna.gz | prodigal -d GCF_008868375.1_ASM886837v1_genomic.fna/cds.fna -a GCF_008868375.1_ASM886837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:58,797] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:58,797] [INFO] Task started: HMMsearch
[2024-01-24 13:13:58,797] [INFO] Running command: hmmsearch --tblout GCF_008868375.1_ASM886837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/reference_markers.hmm GCF_008868375.1_ASM886837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:59,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:59,068] [INFO] Found 6/6 markers.
[2024-01-24 13:13:59,107] [INFO] Query marker FASTA was written to GCF_008868375.1_ASM886837v1_genomic.fna/markers.fasta
[2024-01-24 13:13:59,107] [INFO] Task started: Blastn
[2024-01-24 13:13:59,108] [INFO] Running command: blastn -query GCF_008868375.1_ASM886837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/reference_markers.fasta -out GCF_008868375.1_ASM886837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,148] [INFO] Selected 14 target genomes.
[2024-01-24 13:14:00,148] [INFO] Target genome list was writen to GCF_008868375.1_ASM886837v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:00,168] [INFO] Task started: fastANI
[2024-01-24 13:14:00,169] [INFO] Running command: fastANI --query /var/lib/cwl/stga3575132-6197-4a43-9134-9375025ecab4/GCF_008868375.1_ASM886837v1_genomic.fna.gz --refList GCF_008868375.1_ASM886837v1_genomic.fna/target_genomes.txt --output GCF_008868375.1_ASM886837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:12,215] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:12,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:12,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:12,228] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:12,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:12,228] [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 linens	strain=ATCC 9172	GCA_008868375.1	1703	1703	suspected-type	True	100.0	1261	1269	95	conclusive
Brevibacterium linens	strain=ATCC 9172	GCA_900169165.1	1703	1703	suspected-type	True	99.9971	1262	1269	95	conclusive
Brevibacterium iodinum	strain=ATCC 49514	GCA_900169265.1	31943	31943	type	True	91.5363	972	1269	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	91.4815	1013	1269	95	below_threshold
Brevibacterium pigmentatum	strain=YB235	GCA_011617465.1	1496080	1496080	type	True	91.3502	1039	1269	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	91.0428	1027	1269	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	91.0195	1032	1269	95	below_threshold
Brevibacterium siliguriense	strain=DSM 23676	GCA_900105315.1	1136497	1136497	type	True	89.7617	1008	1269	95	below_threshold
Brevibacterium limosum	strain=o2	GCA_011617705.1	2697565	2697565	type	True	89.6924	1025	1269	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	81.2091	792	1269	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	81.1198	769	1269	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.8392	389	1269	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	77.3465	211	1269	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.642	130	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:12,230] [INFO] DFAST Taxonomy check result was written to GCF_008868375.1_ASM886837v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:12,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:12,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:12,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/checkm_data
[2024-01-24 13:14:12,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:12,273] [INFO] Task started: CheckM
[2024-01-24 13:14:12,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008868375.1_ASM886837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008868375.1_ASM886837v1_genomic.fna/checkm_input GCF_008868375.1_ASM886837v1_genomic.fna/checkm_result
[2024-01-24 13:15:07,237] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:07,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:07,263] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:07,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:07,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008868375.1_ASM886837v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:07,265] [INFO] Task started: Blastn
[2024-01-24 13:15:07,265] [INFO] Running command: blastn -query GCF_008868375.1_ASM886837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d78432-4915-4260-bb9f-03e26ed7dbe9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008868375.1_ASM886837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:08,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:08,801] [INFO] Selected 8 target genomes.
[2024-01-24 13:15:08,801] [INFO] Target genome list was writen to GCF_008868375.1_ASM886837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:08,807] [INFO] Task started: fastANI
[2024-01-24 13:15:08,807] [INFO] Running command: fastANI --query /var/lib/cwl/stga3575132-6197-4a43-9134-9375025ecab4/GCF_008868375.1_ASM886837v1_genomic.fna.gz --refList GCF_008868375.1_ASM886837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008868375.1_ASM886837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:16,931] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:16,945] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:16,945] [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_900169165.1	s__Brevibacterium linens	99.9971	1262	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.12	96.02	0.90	0.82	5	conclusive
GCF_012844365.1	s__Brevibacterium sp012844365	94.247	1055	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169265.1	s__Brevibacterium iodinum	91.5161	974	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013280495.1	s__Brevibacterium permense	91.4815	1013	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011617465.1	s__Brevibacterium sp011617465	91.3396	1039	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623905.1	s__Brevibacterium sediminis	91.0476	1026	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_900105315.1	s__Brevibacterium siliguriense	89.7617	1008	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011617705.1	s__Brevibacterium sp011617705	89.6924	1025	1269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.55	96.55	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:16,947] [INFO] GTDB search result was written to GCF_008868375.1_ASM886837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:16,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:16,951] [INFO] DFAST_QC result json was written to GCF_008868375.1_ASM886837v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:16,951] [INFO] DFAST_QC completed!
[2024-01-24 13:15:16,951] [INFO] Total running time: 0h1m31s