[2024-01-24 13:49:45,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference
[2024-01-24 13:49:46,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,751] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ff5bd1b-1367-40f5-aa4d-3caf199e8a6b/GCF_006385595.1_ASM638559v1_genomic.fna.gz | prodigal -d GCF_006385595.1_ASM638559v1_genomic.fna/cds.fna -a GCF_006385595.1_ASM638559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:07,060] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:07,061] [INFO] Task started: HMMsearch
[2024-01-24 13:50:07,061] [INFO] Running command: hmmsearch --tblout GCF_006385595.1_ASM638559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/reference_markers.hmm GCF_006385595.1_ASM638559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:07,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:07,346] [INFO] Found 6/6 markers.
[2024-01-24 13:50:07,389] [INFO] Query marker FASTA was written to GCF_006385595.1_ASM638559v1_genomic.fna/markers.fasta
[2024-01-24 13:50:07,390] [INFO] Task started: Blastn
[2024-01-24 13:50:07,390] [INFO] Running command: blastn -query GCF_006385595.1_ASM638559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/reference_markers.fasta -out GCF_006385595.1_ASM638559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:08,347] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:08,350] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:08,351] [INFO] Target genome list was writen to GCF_006385595.1_ASM638559v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:08,358] [INFO] Task started: fastANI
[2024-01-24 13:50:08,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff5bd1b-1367-40f5-aa4d-3caf199e8a6b/GCF_006385595.1_ASM638559v1_genomic.fna.gz --refList GCF_006385595.1_ASM638559v1_genomic.fna/target_genomes.txt --output GCF_006385595.1_ASM638559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:20,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:20,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:20,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:20,222] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:20,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:20,222] [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
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	100.0	1536	1536	95	conclusive
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	82.6458	894	1536	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	82.5876	901	1536	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	82.2688	962	1536	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	82.0788	851	1536	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	82.0304	909	1536	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.1657	618	1536	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.9774	587	1536	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.8357	612	1536	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.611	500	1536	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.5094	540	1536	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.8814	544	1536	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.0744	328	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:20,224] [INFO] DFAST Taxonomy check result was written to GCF_006385595.1_ASM638559v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:20,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:20,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:20,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/checkm_data
[2024-01-24 13:50:20,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:20,269] [INFO] Task started: CheckM
[2024-01-24 13:50:20,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385595.1_ASM638559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385595.1_ASM638559v1_genomic.fna/checkm_input GCF_006385595.1_ASM638559v1_genomic.fna/checkm_result
[2024-01-24 13:51:22,176] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:22,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,196] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:22,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:22,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385595.1_ASM638559v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:22,198] [INFO] Task started: Blastn
[2024-01-24 13:51:22,198] [INFO] Running command: blastn -query GCF_006385595.1_ASM638559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45a3141c-4f4e-48c0-8ee6-7f120d852d98/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385595.1_ASM638559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:24,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:24,105] [INFO] Selected 13 target genomes.
[2024-01-24 13:51:24,105] [INFO] Target genome list was writen to GCF_006385595.1_ASM638559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:24,133] [INFO] Task started: fastANI
[2024-01-24 13:51:24,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff5bd1b-1367-40f5-aa4d-3caf199e8a6b/GCF_006385595.1_ASM638559v1_genomic.fna.gz --refList GCF_006385595.1_ASM638559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385595.1_ASM638559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:40,196] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:40,212] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:40,212] [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_006385595.1	s__Luteibacter pinisoli	100.0	1536	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018889975.1	s__Luteibacter sp018889975	85.3072	1122	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964085.1	s__Luteibacter yeojuensis_A	85.19	1074	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110505.1	s__Luteibacter sp900110505	82.834	929	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCA_009912395.1	s__Luteibacter sp009912395	82.8159	914	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829075.1	s__Luteibacter yeojuensis_B	82.7713	958	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011742875.1	s__Luteibacter yeojuensis	82.6456	894	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	82.5877	901	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109915.1	s__Luteibacter sp900109915	82.5591	928	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	82.4738	908	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887595.1	s__Luteibacter rhizovicinus	82.2494	965	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003050935.1	s__Luteibacter sp003050935	82.2136	950	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449605.1	s__Luteibacter sp018449605	81.9794	966	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:40,214] [INFO] GTDB search result was written to GCF_006385595.1_ASM638559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:40,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:40,217] [INFO] DFAST_QC result json was written to GCF_006385595.1_ASM638559v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:40,218] [INFO] DFAST_QC completed!
[2024-01-24 13:51:40,218] [INFO] Total running time: 0h1m55s