[2024-01-24 13:49:27,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,584] [INFO] DQC Reference Directory: /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference
[2024-01-24 13:49:28,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,921] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d2552dc-7114-4c9d-ba0b-51c6231ee3fe/GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/cds.fna -a GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:39,834] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:39,835] [INFO] Task started: HMMsearch
[2024-01-24 13:49:39,835] [INFO] Running command: hmmsearch --tblout GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/reference_markers.hmm GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:40,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:40,125] [INFO] Found 6/6 markers.
[2024-01-24 13:49:40,164] [INFO] Query marker FASTA was written to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:40,165] [INFO] Task started: Blastn
[2024-01-24 13:49:40,165] [INFO] Running command: blastn -query GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/reference_markers.fasta -out GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:41,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:41,281] [INFO] Selected 9 target genomes.
[2024-01-24 13:49:41,281] [INFO] Target genome list was writen to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:41,286] [INFO] Task started: fastANI
[2024-01-24 13:49:41,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2552dc-7114-4c9d-ba0b-51c6231ee3fe/GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna.gz --refList GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:48,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:48,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:48,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:48,244] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:49:48,244] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:48,244] [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
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	100.0	1207	1207	95	inconclusive
Dietzia kunjamensis subsp. schimae	strain=YIM 65001T	GCA_014144975.1	498198	322509	type	True	99.4476	631	1207	95	inconclusive
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	97.1737	1082	1207	95	inconclusive
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	96.674	703	1207	95	inconclusive
Dietzia maris	strain=IMV 195	GCA_009806365.1	37915	37915	suspected-type	True	96.332	674	1207	95	inconclusive
Dietzia maris	strain=IMV 195T	GCA_014144855.1	37915	37915	suspected-type	True	96.2375	651	1207	95	inconclusive
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	86.4478	916	1207	95	below_threshold
Dietzia cinnamea	strain=NBRC 102147	GCA_001571065.1	321318	321318	type	True	86.2872	925	1207	95	below_threshold
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	85.9259	963	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:48,246] [INFO] DFAST Taxonomy check result was written to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:48,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:48,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:48,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/checkm_data
[2024-01-24 13:49:48,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:48,290] [INFO] Task started: CheckM
[2024-01-24 13:49:48,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/checkm_input GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:28,754] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:28,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,781] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:28,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:28,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:28,782] [INFO] Task started: Blastn
[2024-01-24 13:50:28,783] [INFO] Running command: blastn -query GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga59f5962-6c0d-47da-a6b9-37fbedda3a33/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:30,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:30,515] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:30,515] [INFO] Target genome list was writen to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:30,525] [INFO] Task started: fastANI
[2024-01-24 13:50:30,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2552dc-7114-4c9d-ba0b-51c6231ee3fe/GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna.gz --refList GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:36,994] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,007] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:37,007] [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_014144855.1	s__Dietzia maris	96.2102	651	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	86.7153	843	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
GCF_001571065.1	s__Dietzia cinnamea	86.2744	927	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	-
GCF_008369165.1	s__Dietzia sp008369165	86.196	899	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096075.1	s__Dietzia lutea	85.9259	963	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014145145.1	s__Dietzia cercidiphylli	84.5632	618	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.02	96.60	0.78	0.68	10	-
GCA_002415925.1	s__Dietzia sp002415925	84.1208	746	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	83.4581	872	1207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,010] [INFO] GTDB search result was written to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:37,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:37,015] [INFO] DFAST_QC result json was written to GCF_900182685.1_IMG-taxon_2724679793_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:37,015] [INFO] DFAST_QC completed!
[2024-01-24 13:50:37,016] [INFO] Total running time: 0h1m9s