[2024-01-24 15:26:54,399] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference
[2024-01-24 15:26:55,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:55,782] [INFO] Task started: Prodigal
[2024-01-24 15:26:55,783] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7a76216-8d70-4460-af30-1a6b909892ba/GCF_016026595.1_ASM1602659v1_genomic.fna.gz | prodigal -d GCF_016026595.1_ASM1602659v1_genomic.fna/cds.fna -a GCF_016026595.1_ASM1602659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:07,236] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:07,237] [INFO] Task started: HMMsearch
[2024-01-24 15:27:07,237] [INFO] Running command: hmmsearch --tblout GCF_016026595.1_ASM1602659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/reference_markers.hmm GCF_016026595.1_ASM1602659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:07,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:07,491] [INFO] Found 6/6 markers.
[2024-01-24 15:27:07,533] [INFO] Query marker FASTA was written to GCF_016026595.1_ASM1602659v1_genomic.fna/markers.fasta
[2024-01-24 15:27:07,533] [INFO] Task started: Blastn
[2024-01-24 15:27:07,534] [INFO] Running command: blastn -query GCF_016026595.1_ASM1602659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/reference_markers.fasta -out GCF_016026595.1_ASM1602659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:08,815] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:08,818] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:08,819] [INFO] Target genome list was writen to GCF_016026595.1_ASM1602659v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:08,827] [INFO] Task started: fastANI
[2024-01-24 15:27:08,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7a76216-8d70-4460-af30-1a6b909892ba/GCF_016026595.1_ASM1602659v1_genomic.fna.gz --refList GCF_016026595.1_ASM1602659v1_genomic.fna/target_genomes.txt --output GCF_016026595.1_ASM1602659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:27,146] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:27,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:27,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:27,162] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:27,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:27,163] [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 casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	100.0	1288	1288	95	conclusive
Brevibacterium casei	strain=CIP 102111	GCA_900169275.1	33889	33889	type	True	99.9863	1268	1288	95	conclusive
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	82.1185	801	1288	95	below_threshold
Brevibacterium oceani	strain=BBH7	GCA_013623835.1	358099	358099	type	True	81.9887	828	1288	95	below_threshold
Brevibacterium pigmentatum	strain=YB235	GCA_011617465.1	1496080	1496080	type	True	81.5975	778	1288	95	below_threshold
Brevibacterium renqingii	strain=REN4	GCA_017808105.1	2776916	2776916	type	True	81.5752	761	1288	95	below_threshold
Brevibacterium limosum	strain=o2	GCA_011617705.1	2697565	2697565	type	True	81.4649	788	1288	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	81.4372	755	1288	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_008868375.1	1703	1703	suspected-type	True	81.3687	771	1288	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	81.3441	797	1288	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	81.3238	799	1288	95	below_threshold
Brevibacterium iodinum	strain=ATCC 49514	GCA_900169265.1	31943	31943	type	True	81.2279	728	1288	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	80.3911	737	1288	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	80.3499	723	1288	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.9051	203	1288	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.7788	216	1288	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	76.753	225	1288	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	76.5701	226	1288	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	76.1956	50	1288	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	76.1276	50	1288	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	76.0297	51	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:27,164] [INFO] DFAST Taxonomy check result was written to GCF_016026595.1_ASM1602659v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:27,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:27,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:27,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/checkm_data
[2024-01-24 15:27:27,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:27,205] [INFO] Task started: CheckM
[2024-01-24 15:27:27,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016026595.1_ASM1602659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016026595.1_ASM1602659v1_genomic.fna/checkm_input GCF_016026595.1_ASM1602659v1_genomic.fna/checkm_result
[2024-01-24 15:28:22,814] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:22,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:22,832] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:22,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:22,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016026595.1_ASM1602659v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:22,833] [INFO] Task started: Blastn
[2024-01-24 15:28:22,833] [INFO] Running command: blastn -query GCF_016026595.1_ASM1602659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb278e902-7a45-4149-96de-c20bb7b84616/dqc_reference/reference_markers_gtdb.fasta -out GCF_016026595.1_ASM1602659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:24,595] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:24,598] [INFO] Selected 15 target genomes.
[2024-01-24 15:28:24,598] [INFO] Target genome list was writen to GCF_016026595.1_ASM1602659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:24,608] [INFO] Task started: fastANI
[2024-01-24 15:28:24,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7a76216-8d70-4460-af30-1a6b909892ba/GCF_016026595.1_ASM1602659v1_genomic.fna.gz --refList GCF_016026595.1_ASM1602659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016026595.1_ASM1602659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:38,337] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:38,350] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:38,350] [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_900169275.1	s__Brevibacterium casei	99.9863	1268	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.23	97.33	0.93	0.90	17	conclusive
GCF_006489205.1	s__Brevibacterium sp006489205	87.5312	1066	1288	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	86.827	1059	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.80	97.80	0.94	0.94	2	-
GCF_003315415.1	s__Brevibacterium celere_A	82.6561	801	1288	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	82.1132	800	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623835.1	s__Brevibacterium oceani	81.9887	828	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.48	96.48	0.86	0.86	2	-
GCF_017808105.1	s__Brevibacterium renqingii	81.6039	758	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_011617465.1	s__Brevibacterium sp011617465	81.579	778	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844365.1	s__Brevibacterium sp012844365	81.4968	821	1288	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	81.4424	785	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.55	96.55	0.87	0.87	2	-
GCF_900169165.1	s__Brevibacterium linens	81.4048	768	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.12	96.02	0.90	0.82	5	-
GCF_013623905.1	s__Brevibacterium sediminis	81.3356	798	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_015142735.1	s__Oerskovia sp015142735	76.7618	223	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719775.1	s__Streptomyces sp000719775	75.9866	187	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360825.1	s__WSZJ01 sp013360825	74.8484	53	1288	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__WSZJ01;g__WSZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:38,352] [INFO] GTDB search result was written to GCF_016026595.1_ASM1602659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:38,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:38,359] [INFO] DFAST_QC result json was written to GCF_016026595.1_ASM1602659v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:38,359] [INFO] DFAST_QC completed!
[2024-01-24 15:28:38,359] [INFO] Total running time: 0h1m44s