[2024-01-25 19:41:35,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:35,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:35,602] [INFO] DQC Reference Directory: /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference
[2024-01-25 19:41:36,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:36,773] [INFO] Task started: Prodigal
[2024-01-25 19:41:36,773] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6da270a-dc6b-4474-b47c-6da682b2c12e/GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/cds.fna -a GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:04,151] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:04,152] [INFO] Task started: HMMsearch
[2024-01-25 19:42:04,152] [INFO] Running command: hmmsearch --tblout GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/reference_markers.hmm GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:04,525] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:04,526] [INFO] Found 6/6 markers.
[2024-01-25 19:42:04,601] [INFO] Query marker FASTA was written to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:42:04,601] [INFO] Task started: Blastn
[2024-01-25 19:42:04,602] [INFO] Running command: blastn -query GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/reference_markers.fasta -out GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:05,982] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:05,985] [INFO] Selected 17 target genomes.
[2024-01-25 19:42:05,985] [INFO] Target genome list was writen to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:42:06,017] [INFO] Task started: fastANI
[2024-01-25 19:42:06,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6da270a-dc6b-4474-b47c-6da682b2c12e/GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna.gz --refList GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:54,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:54,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:54,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:54,237] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:54,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:54,238] [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 wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	100.0	3329	3331	95	conclusive
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	94.0586	2544	3331	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	94.044	2531	3331	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.3786	2119	3331	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.2005	2009	3331	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.161	2123	3331	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.0486	2282	3331	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	84.8918	2136	3331	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	84.8901	2119	3331	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	84.8102	2284	3331	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	84.7637	1858	3331	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	84.731	2276	3331	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	84.2934	1901	3331	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.7287	1238	3331	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	83.6067	1888	3331	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.1681	1775	3331	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.7674	1989	3331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:54,239] [INFO] DFAST Taxonomy check result was written to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:42:54,244] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:54,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:54,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/checkm_data
[2024-01-25 19:42:54,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:54,334] [INFO] Task started: CheckM
[2024-01-25 19:42:54,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/checkm_input GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:44:35,430] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:35,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-25 19:44:35,468] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:35,468] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:35,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:44:35,469] [INFO] Task started: Blastn
[2024-01-25 19:44:35,469] [INFO] Running command: blastn -query GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga3ccf30e-c9c3-46b6-9beb-cdf011fc5fad/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:37,743] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:37,746] [INFO] Selected 15 target genomes.
[2024-01-25 19:44:37,746] [INFO] Target genome list was writen to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:37,763] [INFO] Task started: fastANI
[2024-01-25 19:44:37,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6da270a-dc6b-4474-b47c-6da682b2c12e/GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna.gz --refList GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:21,899] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:21,908] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:21,908] [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_900111685.1	s__Nonomuraea wenchangensis	100.0	3329	3331	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_000379885.1	s__Nonomuraea coxensis	94.057	2529	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.4751	2183	3331	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	85.353	2125	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	85.1866	2118	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	85.169	2016	3331	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	84.8499	2324	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014873145.1	s__Nonomuraea angiospora	84.8119	2283	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	84.7647	1858	3331	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	84.7266	2275	3331	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	84.7117	2247	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.3347	2107	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_001083785.1	s__Nonomuraea sp001083785	83.6436	1898	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	83.2153	1766	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	83.0572	1861	3331	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:21,909] [INFO] GTDB search result was written to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:21,910] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:21,913] [INFO] DFAST_QC result json was written to GCF_900111685.1_IMG-taxon_2675903060_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:45:21,913] [INFO] DFAST_QC completed!
[2024-01-25 19:45:21,914] [INFO] Total running time: 0h3m46s