[2024-01-24 14:22:17,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference
[2024-01-24 14:22:18,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,398] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dd8c293-cea9-4b63-8085-ab96249dcfdb/GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/cds.fna -a GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:55,701] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:55,702] [INFO] Task started: HMMsearch
[2024-01-24 14:22:55,702] [INFO] Running command: hmmsearch --tblout GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/reference_markers.hmm GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:56,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:56,177] [INFO] Found 6/6 markers.
[2024-01-24 14:22:56,274] [INFO] Query marker FASTA was written to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:56,275] [INFO] Task started: Blastn
[2024-01-24 14:22:56,275] [INFO] Running command: blastn -query GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/reference_markers.fasta -out GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:57,636] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:57,646] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:57,647] [INFO] Target genome list was writen to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:57,653] [INFO] Task started: fastANI
[2024-01-24 14:22:57,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd8c293-cea9-4b63-8085-ab96249dcfdb/GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna.gz --refList GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:45,116] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:45,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:45,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:45,130] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:45,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:45,130] [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
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	100.0	4370	4376	95	conclusive
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	86.6759	2883	4376	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	86.4206	2515	4376	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	86.3674	2648	4376	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	86.2586	2639	4376	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	86.1128	2780	4376	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	86.076	2797	4376	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.9947	2609	4376	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.5868	2326	4376	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.4721	2257	4376	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.2288	2398	4376	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.2045	2396	4376	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.1287	2325	4376	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.9692	1306	4376	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	82.717	2074	4376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:45,133] [INFO] DFAST Taxonomy check result was written to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:23:45,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:45,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:45,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/checkm_data
[2024-01-24 14:23:45,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:45,251] [INFO] Task started: CheckM
[2024-01-24 14:23:45,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/checkm_input GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:25:53,846] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:53,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 7.06%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:25:53,879] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:53,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:53,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:25:53,880] [INFO] Task started: Blastn
[2024-01-24 14:25:53,880] [INFO] Running command: blastn -query GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00677dae-39fa-4d3e-b1df-8470f7ff7887/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:56,010] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:56,014] [INFO] Selected 13 target genomes.
[2024-01-24 14:25:56,014] [INFO] Target genome list was writen to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:56,049] [INFO] Task started: fastANI
[2024-01-24 14:25:56,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd8c293-cea9-4b63-8085-ab96249dcfdb/GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna.gz --refList GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:40,717] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:40,734] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:40,735] [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_900108335.1	s__Nonomuraea solani	100.0	4370	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014207985.1	s__Nonomuraea rubra	86.6462	2890	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889725.1	s__Nonomuraea zeae	86.3927	2643	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	86.2722	2635	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	86.0918	2786	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	86.0566	2864	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	86.0348	2808	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	86.019	2602	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	85.8356	2829	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_004348685.1	s__Nonomuraea deserti	85.5625	2332	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.5208	2579	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348995.1	s__Nonomuraea terrae	85.455	2108	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	83.6076	2174	4376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:40,737] [INFO] GTDB search result was written to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:40,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:40,742] [INFO] DFAST_QC result json was written to GCF_900108335.1_IMG-taxon_2675903140_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:26:40,742] [INFO] DFAST_QC completed!
[2024-01-24 14:26:40,742] [INFO] Total running time: 0h4m24s