[2024-01-25 19:08:50,587] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:50,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:50,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference
[2024-01-25 19:08:51,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:51,725] [INFO] Task started: Prodigal
[2024-01-25 19:08:51,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg9553f613-9f50-40fd-9afe-b79a35d26d7c/GCF_017808105.1_ASM1780810v1_genomic.fna.gz | prodigal -d GCF_017808105.1_ASM1780810v1_genomic.fna/cds.fna -a GCF_017808105.1_ASM1780810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:00,992] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:00,992] [INFO] Task started: HMMsearch
[2024-01-25 19:09:00,992] [INFO] Running command: hmmsearch --tblout GCF_017808105.1_ASM1780810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/reference_markers.hmm GCF_017808105.1_ASM1780810v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:01,228] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:01,229] [INFO] Found 6/6 markers.
[2024-01-25 19:09:01,256] [INFO] Query marker FASTA was written to GCF_017808105.1_ASM1780810v1_genomic.fna/markers.fasta
[2024-01-25 19:09:01,257] [INFO] Task started: Blastn
[2024-01-25 19:09:01,257] [INFO] Running command: blastn -query GCF_017808105.1_ASM1780810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/reference_markers.fasta -out GCF_017808105.1_ASM1780810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:02,299] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:02,301] [INFO] Selected 18 target genomes.
[2024-01-25 19:09:02,302] [INFO] Target genome list was writen to GCF_017808105.1_ASM1780810v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:02,305] [INFO] Task started: fastANI
[2024-01-25 19:09:02,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg9553f613-9f50-40fd-9afe-b79a35d26d7c/GCF_017808105.1_ASM1780810v1_genomic.fna.gz --refList GCF_017808105.1_ASM1780810v1_genomic.fna/target_genomes.txt --output GCF_017808105.1_ASM1780810v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:16,703] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:16,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:16,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:16,715] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:16,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:16,715] [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 renqingii	strain=REN4	GCA_017808105.1	2776916	2776916	type	True	100.0	1193	1193	95	conclusive
Brevibacterium limosum	strain=o2	GCA_011617705.1	2697565	2697565	type	True	85.1024	978	1193	95	below_threshold
Brevibacterium oceani	strain=BBH7	GCA_013623835.1	358099	358099	type	True	84.9535	940	1193	95	below_threshold
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	84.9009	913	1193	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_008868375.1	1703	1703	suspected-type	True	84.8036	906	1193	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_900169165.1	1703	1703	suspected-type	True	84.7882	915	1193	95	below_threshold
Brevibacterium epidermidis	strain=NBRC 14811	GCA_001570805.1	1698	1698	type	True	84.6782	898	1193	95	below_threshold
Brevibacterium pigmentatum	strain=YB235	GCA_011617465.1	1496080	1496080	type	True	84.6699	940	1193	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	84.5502	923	1193	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	84.5166	889	1193	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	84.5059	919	1193	95	below_threshold
Brevibacterium iodinum	strain=ATCC 49514	GCA_900169265.1	31943	31943	type	True	84.4663	886	1193	95	below_threshold
Brevibacterium siliguriense	strain=DSM 23676	GCA_900105315.1	1136497	1136497	type	True	84.2991	953	1193	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	81.2394	777	1193	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	81.2191	770	1193	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.7612	394	1193	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	78.2174	327	1193	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	76.4637	153	1193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:16,717] [INFO] DFAST Taxonomy check result was written to GCF_017808105.1_ASM1780810v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:16,717] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:16,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:16,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/checkm_data
[2024-01-25 19:09:16,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:16,756] [INFO] Task started: CheckM
[2024-01-25 19:09:16,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017808105.1_ASM1780810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017808105.1_ASM1780810v1_genomic.fna/checkm_input GCF_017808105.1_ASM1780810v1_genomic.fna/checkm_result
[2024-01-25 19:10:07,782] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:07,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:07,821] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:07,821] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:07,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017808105.1_ASM1780810v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:07,822] [INFO] Task started: Blastn
[2024-01-25 19:10:07,822] [INFO] Running command: blastn -query GCF_017808105.1_ASM1780810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d75bba1-c790-420b-a14a-e5cddb790dc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017808105.1_ASM1780810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:09,501] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:09,504] [INFO] Selected 14 target genomes.
[2024-01-25 19:10:09,505] [INFO] Target genome list was writen to GCF_017808105.1_ASM1780810v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:09,512] [INFO] Task started: fastANI
[2024-01-25 19:10:09,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg9553f613-9f50-40fd-9afe-b79a35d26d7c/GCF_017808105.1_ASM1780810v1_genomic.fna.gz --refList GCF_017808105.1_ASM1780810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017808105.1_ASM1780810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:21,751] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:21,760] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:21,760] [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_017808105.1	s__Brevibacterium renqingii	100.0	1193	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.54	98.54	0.94	0.94	2	conclusive
GCA_019117545.1	s__Brevibacterium intestinavium	88.1905	828	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.71	98.71	0.97	0.97	2	-
GCF_004745075.1	s__Brevibacterium sp004745075	85.1925	940	1193	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	85.0806	980	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.55	96.55	0.87	0.87	2	-
GCF_013623835.1	s__Brevibacterium oceani	84.951	940	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.48	96.48	0.86	0.86	2	-
GCF_011617245.1	s__Brevibacterium sp011617245	84.9009	913	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169165.1	s__Brevibacterium linens	84.7959	914	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.12	96.02	0.90	0.82	5	-
GCF_012844365.1	s__Brevibacterium sp012844365	84.7401	946	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570805.1	s__Brevibacterium epidermidis	84.6895	897	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.16	95.79	0.90	0.89	4	-
GCF_011617465.1	s__Brevibacterium sp011617465	84.687	938	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280495.1	s__Brevibacterium permense	84.5101	889	1193	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	84.5056	919	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_900169265.1	s__Brevibacterium iodinum	84.4555	887	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105315.1	s__Brevibacterium siliguriense	84.2991	953	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:21,762] [INFO] GTDB search result was written to GCF_017808105.1_ASM1780810v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:21,762] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:21,767] [INFO] DFAST_QC result json was written to GCF_017808105.1_ASM1780810v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:21,767] [INFO] DFAST_QC completed!
[2024-01-25 19:10:21,767] [INFO] Total running time: 0h1m31s