[2024-01-24 12:07:06,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference
[2024-01-24 12:07:08,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,031] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgfff04865-1add-43fa-8172-6102c9ef6dbf/GCF_014836885.1_ASM1483688v1_genomic.fna.gz | prodigal -d GCF_014836885.1_ASM1483688v1_genomic.fna/cds.fna -a GCF_014836885.1_ASM1483688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:17,247] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:17,247] [INFO] Task started: HMMsearch
[2024-01-24 12:07:17,248] [INFO] Running command: hmmsearch --tblout GCF_014836885.1_ASM1483688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/reference_markers.hmm GCF_014836885.1_ASM1483688v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:17,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:17,538] [INFO] Found 6/6 markers.
[2024-01-24 12:07:17,602] [INFO] Query marker FASTA was written to GCF_014836885.1_ASM1483688v1_genomic.fna/markers.fasta
[2024-01-24 12:07:17,602] [INFO] Task started: Blastn
[2024-01-24 12:07:17,603] [INFO] Running command: blastn -query GCF_014836885.1_ASM1483688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/reference_markers.fasta -out GCF_014836885.1_ASM1483688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:18,717] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:18,721] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:18,722] [INFO] Target genome list was writen to GCF_014836885.1_ASM1483688v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:18,726] [INFO] Task started: fastANI
[2024-01-24 12:07:18,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgfff04865-1add-43fa-8172-6102c9ef6dbf/GCF_014836885.1_ASM1483688v1_genomic.fna.gz --refList GCF_014836885.1_ASM1483688v1_genomic.fna/target_genomes.txt --output GCF_014836885.1_ASM1483688v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:27,564] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:27,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:27,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:27,578] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:27,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:27,578] [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 gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	100.0	1035	1037	95	conclusive
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	93.4895	874	1037	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	93.4457	875	1037	95	below_threshold
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	79.9925	520	1037	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	79.6041	425	1037	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	79.4582	420	1037	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	79.3973	444	1037	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	78.3253	315	1037	95	below_threshold
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	78.284	360	1037	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	78.1341	268	1037	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	77.9735	320	1037	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	76.189	185	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:27,581] [INFO] DFAST Taxonomy check result was written to GCF_014836885.1_ASM1483688v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:27,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:27,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:27,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/checkm_data
[2024-01-24 12:07:27,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:27,622] [INFO] Task started: CheckM
[2024-01-24 12:07:27,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836885.1_ASM1483688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836885.1_ASM1483688v1_genomic.fna/checkm_input GCF_014836885.1_ASM1483688v1_genomic.fna/checkm_result
[2024-01-24 12:08:15,289] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:15,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:15,311] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:15,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:15,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836885.1_ASM1483688v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:15,312] [INFO] Task started: Blastn
[2024-01-24 12:08:15,312] [INFO] Running command: blastn -query GCF_014836885.1_ASM1483688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82328e17-5336-4df8-b326-c785f82e72ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836885.1_ASM1483688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:16,989] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:16,993] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:16,993] [INFO] Target genome list was writen to GCF_014836885.1_ASM1483688v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:17,000] [INFO] Task started: fastANI
[2024-01-24 12:08:17,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgfff04865-1add-43fa-8172-6102c9ef6dbf/GCF_014836885.1_ASM1483688v1_genomic.fna.gz --refList GCF_014836885.1_ASM1483688v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836885.1_ASM1483688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:23,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:23,316] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:23,316] [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_013359525.1	s__Brevibacterium luteolum_A	96.2493	872	1037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	conclusive
GCF_013004595.1	s__Brevibacterium luteolum	93.4729	875	1037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	-
GCF_005280295.1	s__Brevibacterium sp005280295	80.3999	543	1037	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	80.0247	517	1037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006489205.1	s__Brevibacterium sp006489205	79.6042	416	1037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.50	98.50	0.93	0.93	2	-
GCF_009857845.1	s__Brevibacterium rongguiense	79.5994	425	1037	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	79.3085	454	1037	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	78.9847	419	1037	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	78.2435	265	1037	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 12:08:23,318] [INFO] GTDB search result was written to GCF_014836885.1_ASM1483688v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:23,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:23,321] [INFO] DFAST_QC result json was written to GCF_014836885.1_ASM1483688v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:23,321] [INFO] DFAST_QC completed!
[2024-01-24 12:08:23,321] [INFO] Total running time: 0h1m17s