[2024-01-25 18:48:35,870] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,871] [INFO] DQC Reference Directory: /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference
[2024-01-25 18:48:36,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,991] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,991] [INFO] Running command: gunzip -c /var/lib/cwl/stgc87993cf-9ce8-4905-ad7a-daf2ac7ac846/GCF_009857845.1_ASM985784v1_genomic.fna.gz | prodigal -d GCF_009857845.1_ASM985784v1_genomic.fna/cds.fna -a GCF_009857845.1_ASM985784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:44,312] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:44,312] [INFO] Task started: HMMsearch
[2024-01-25 18:48:44,313] [INFO] Running command: hmmsearch --tblout GCF_009857845.1_ASM985784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/reference_markers.hmm GCF_009857845.1_ASM985784v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:44,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:44,509] [INFO] Found 6/6 markers.
[2024-01-25 18:48:44,533] [INFO] Query marker FASTA was written to GCF_009857845.1_ASM985784v1_genomic.fna/markers.fasta
[2024-01-25 18:48:44,533] [INFO] Task started: Blastn
[2024-01-25 18:48:44,534] [INFO] Running command: blastn -query GCF_009857845.1_ASM985784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/reference_markers.fasta -out GCF_009857845.1_ASM985784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:45,726] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:45,729] [INFO] Selected 15 target genomes.
[2024-01-25 18:48:45,730] [INFO] Target genome list was writen to GCF_009857845.1_ASM985784v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:45,748] [INFO] Task started: fastANI
[2024-01-25 18:48:45,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87993cf-9ce8-4905-ad7a-daf2ac7ac846/GCF_009857845.1_ASM985784v1_genomic.fna.gz --refList GCF_009857845.1_ASM985784v1_genomic.fna/target_genomes.txt --output GCF_009857845.1_ASM985784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:56,244] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:56,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:56,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:56,254] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:56,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:56,254] [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 rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	100.0	958	966	95	conclusive
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	80.1424	471	966	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	79.636	384	966	95	below_threshold
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	79.5788	398	966	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	79.478	440	966	95	below_threshold
Brevibacterium album	strain=DSM 18261	GCA_000426445.1	417948	417948	type	True	79.2185	439	966	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	79.1685	411	966	95	below_threshold
Brevibacterium casei	strain=CIP 102111	GCA_900169275.1	33889	33889	type	True	79.098	419	966	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	79.0178	397	966	95	below_threshold
Brevibacterium jeotgali	strain=SJ5-8	GCA_900169175.1	1262550	1262550	type	True	78.4948	341	966	95	below_threshold
Brevibacterium jeotgali	strain=DSM 29217	GCA_007828155.1	1262550	1262550	type	True	78.4779	336	966	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	78.0758	267	966	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.0681	235	966	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.9596	248	966	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	76.1261	264	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:56,256] [INFO] DFAST Taxonomy check result was written to GCF_009857845.1_ASM985784v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:56,256] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:56,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:56,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/checkm_data
[2024-01-25 18:48:56,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:56,288] [INFO] Task started: CheckM
[2024-01-25 18:48:56,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009857845.1_ASM985784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009857845.1_ASM985784v1_genomic.fna/checkm_input GCF_009857845.1_ASM985784v1_genomic.fna/checkm_result
[2024-01-25 18:49:34,455] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:34,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:34,482] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:34,482] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:34,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009857845.1_ASM985784v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:34,483] [INFO] Task started: Blastn
[2024-01-25 18:49:34,483] [INFO] Running command: blastn -query GCF_009857845.1_ASM985784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec1ac60-949d-41df-9d88-d0b774e5a6cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009857845.1_ASM985784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:36,666] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:36,670] [INFO] Selected 12 target genomes.
[2024-01-25 18:49:36,670] [INFO] Target genome list was writen to GCF_009857845.1_ASM985784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:36,680] [INFO] Task started: fastANI
[2024-01-25 18:49:36,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgc87993cf-9ce8-4905-ad7a-daf2ac7ac846/GCF_009857845.1_ASM985784v1_genomic.fna.gz --refList GCF_009857845.1_ASM985784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009857845.1_ASM985784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:46,204] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:46,212] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:46,212] [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_009857845.1	s__Brevibacterium rongguiense	100.0	958	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005280295.1	s__Brevibacterium sp005280295	80.343	504	966	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	80.1529	471	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359525.1	s__Brevibacterium luteolum_A	79.6132	423	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	-
GCF_013004595.1	s__Brevibacterium luteolum	79.579	398	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	-
GCF_000426445.1	s__Brevibacterium album	79.2604	435	966	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	79.2299	418	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.50	98.50	0.93	0.93	2	-
GCF_003315415.1	s__Brevibacterium celere_A	79.1185	397	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900169275.1	s__Brevibacterium casei	79.1098	418	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.23	97.33	0.93	0.90	17	-
GCF_018137945.1	s__Brevibacterium sp018137945	79.0818	436	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.80	97.80	0.94	0.94	2	-
GCF_900163715.1	s__Brevibacterium yomogidense_A	78.7201	363	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.08	97.08	0.87	0.87	2	-
GCF_000787835.1	s__Streptacidiphilus melanogenes	76.0989	265	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:46,214] [INFO] GTDB search result was written to GCF_009857845.1_ASM985784v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:46,214] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:46,217] [INFO] DFAST_QC result json was written to GCF_009857845.1_ASM985784v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:46,217] [INFO] DFAST_QC completed!
[2024-01-25 18:49:46,217] [INFO] Total running time: 0h1m10s