[2024-01-24 13:18:46,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference
[2024-01-24 13:18:47,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,789] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgb46e7e43-5f37-48e4-a9db-69a7186b2e7d/GCF_013004595.1_ASM1300459v1_genomic.fna.gz | prodigal -d GCF_013004595.1_ASM1300459v1_genomic.fna/cds.fna -a GCF_013004595.1_ASM1300459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:56,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:56,960] [INFO] Task started: HMMsearch
[2024-01-24 13:18:56,960] [INFO] Running command: hmmsearch --tblout GCF_013004595.1_ASM1300459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/reference_markers.hmm GCF_013004595.1_ASM1300459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:57,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:57,180] [INFO] Found 6/6 markers.
[2024-01-24 13:18:57,208] [INFO] Query marker FASTA was written to GCF_013004595.1_ASM1300459v1_genomic.fna/markers.fasta
[2024-01-24 13:18:57,208] [INFO] Task started: Blastn
[2024-01-24 13:18:57,208] [INFO] Running command: blastn -query GCF_013004595.1_ASM1300459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/reference_markers.fasta -out GCF_013004595.1_ASM1300459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:58,293] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:58,296] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:58,297] [INFO] Target genome list was writen to GCF_013004595.1_ASM1300459v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:58,314] [INFO] Task started: fastANI
[2024-01-24 13:18:58,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46e7e43-5f37-48e4-a9db-69a7186b2e7d/GCF_013004595.1_ASM1300459v1_genomic.fna.gz --refList GCF_013004595.1_ASM1300459v1_genomic.fna/target_genomes.txt --output GCF_013004595.1_ASM1300459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:07,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:07,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:07,723] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:07,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:07,723] [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 luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	100.0	976	976	95	conclusive
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	99.994	975	976	95	conclusive
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	93.4583	864	976	95	below_threshold
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	80.1377	518	976	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	79.414	405	976	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	79.2546	430	976	95	below_threshold
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	78.7457	401	976	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	78.5576	388	976	95	below_threshold
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	78.5499	360	976	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	77.9881	330	976	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	77.9353	281	976	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	76.7171	156	976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:07,725] [INFO] DFAST Taxonomy check result was written to GCF_013004595.1_ASM1300459v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:07,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:07,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:07,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/checkm_data
[2024-01-24 13:19:07,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:07,759] [INFO] Task started: CheckM
[2024-01-24 13:19:07,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013004595.1_ASM1300459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013004595.1_ASM1300459v1_genomic.fna/checkm_input GCF_013004595.1_ASM1300459v1_genomic.fna/checkm_result
[2024-01-24 13:19:52,409] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:52,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,430] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:52,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:52,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013004595.1_ASM1300459v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:52,431] [INFO] Task started: Blastn
[2024-01-24 13:19:52,431] [INFO] Running command: blastn -query GCF_013004595.1_ASM1300459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d1d3528-a070-444e-9bb8-8119cd6fe3cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_013004595.1_ASM1300459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:54,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:54,250] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:54,250] [INFO] Target genome list was writen to GCF_013004595.1_ASM1300459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:54,268] [INFO] Task started: fastANI
[2024-01-24 13:19:54,268] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46e7e43-5f37-48e4-a9db-69a7186b2e7d/GCF_013004595.1_ASM1300459v1_genomic.fna.gz --refList GCF_013004595.1_ASM1300459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013004595.1_ASM1300459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:01,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:01,959] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:01,959] [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_013004595.1	s__Brevibacterium luteolum	100.0	976	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	conclusive
GCF_013359525.1	s__Brevibacterium luteolum_A	93.7027	847	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	-
GCF_005280295.1	s__Brevibacterium sp005280295	80.4553	543	976	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	80.126	517	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857845.1	s__Brevibacterium rongguiense	79.3902	407	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137945.1	s__Brevibacterium sp018137945	79.1284	442	976	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	78.9061	407	976	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	78.7349	402	976	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	78.6058	388	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_000285835.1	s__Brevibacterium senegalense	78.5382	361	976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019117325.1	s__Brevibacterium intestinigallinarum	78.2921	249	976	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 13:20:01,964] [INFO] GTDB search result was written to GCF_013004595.1_ASM1300459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:01,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:01,970] [INFO] DFAST_QC result json was written to GCF_013004595.1_ASM1300459v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:01,970] [INFO] DFAST_QC completed!
[2024-01-24 13:20:01,970] [INFO] Total running time: 0h1m15s