[2024-01-24 14:28:08,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference
[2024-01-24 14:28:10,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,422] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bb1296b-9d3e-4e15-bfbc-b73651b07932/GCF_013283785.1_ASM1328378v1_genomic.fna.gz | prodigal -d GCF_013283785.1_ASM1328378v1_genomic.fna/cds.fna -a GCF_013283785.1_ASM1328378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:42,513] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:42,513] [INFO] Task started: HMMsearch
[2024-01-24 14:28:42,513] [INFO] Running command: hmmsearch --tblout GCF_013283785.1_ASM1328378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/reference_markers.hmm GCF_013283785.1_ASM1328378v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:43,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:43,090] [INFO] Found 6/6 markers.
[2024-01-24 14:28:43,192] [INFO] Query marker FASTA was written to GCF_013283785.1_ASM1328378v1_genomic.fna/markers.fasta
[2024-01-24 14:28:43,193] [INFO] Task started: Blastn
[2024-01-24 14:28:43,193] [INFO] Running command: blastn -query GCF_013283785.1_ASM1328378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/reference_markers.fasta -out GCF_013283785.1_ASM1328378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:44,746] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:44,754] [INFO] Selected 20 target genomes.
[2024-01-24 14:28:44,755] [INFO] Target genome list was writen to GCF_013283785.1_ASM1328378v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:44,779] [INFO] Task started: fastANI
[2024-01-24 14:28:44,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb1296b-9d3e-4e15-bfbc-b73651b07932/GCF_013283785.1_ASM1328378v1_genomic.fna.gz --refList GCF_013283785.1_ASM1328378v1_genomic.fna/target_genomes.txt --output GCF_013283785.1_ASM1328378v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:43,456] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:43,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:43,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:43,478] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:43,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:43,479] [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 antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	100.0	3579	3601	95	conclusive
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.3826	2177	3601	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	84.0138	2111	3601	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	83.9655	2284	3601	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.9545	1225	3601	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.7739	2044	3601	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.653	2105	3601	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	83.6425	2137	3601	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	83.6278	1749	3601	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	83.5548	1873	3601	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.5491	1986	3601	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	83.5464	1877	3601	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	83.54	1973	3601	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	83.4509	1999	3601	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	83.4296	1869	3601	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	83.4253	1945	3601	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	83.3631	1833	3601	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	83.1566	1835	3601	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	82.8536	1769	3601	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.813	1957	3601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:43,480] [INFO] DFAST Taxonomy check result was written to GCF_013283785.1_ASM1328378v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:43,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:43,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:43,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/checkm_data
[2024-01-24 14:29:43,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:43,586] [INFO] Task started: CheckM
[2024-01-24 14:29:43,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283785.1_ASM1328378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283785.1_ASM1328378v1_genomic.fna/checkm_input GCF_013283785.1_ASM1328378v1_genomic.fna/checkm_result
[2024-01-24 14:31:23,057] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:23,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.84%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:31:23,084] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:23,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:23,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283785.1_ASM1328378v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:23,085] [INFO] Task started: Blastn
[2024-01-24 14:31:23,085] [INFO] Running command: blastn -query GCF_013283785.1_ASM1328378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb213b25f-ba9d-42de-9c97-d1acc9793537/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283785.1_ASM1328378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:25,420] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:25,424] [INFO] Selected 19 target genomes.
[2024-01-24 14:31:25,424] [INFO] Target genome list was writen to GCF_013283785.1_ASM1328378v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:25,438] [INFO] Task started: fastANI
[2024-01-24 14:31:25,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb1296b-9d3e-4e15-bfbc-b73651b07932/GCF_013283785.1_ASM1328378v1_genomic.fna.gz --refList GCF_013283785.1_ASM1328378v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283785.1_ASM1328378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:25,498] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:25,514] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:25,515] [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_013283785.1	s__Nonomuraea sp013283785	100.0	3579	3601	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_014648435.1	s__Nonomuraea spiralis	84.3801	2179	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_005889725.1	s__Nonomuraea zeae	84.0141	2111	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	83.9542	2287	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	83.8293	2137	3601	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	83.7817	2214	3601	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	83.7735	2045	3601	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	83.7407	2240	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014204795.1	s__Nonomuraea jabiensis	83.6713	2133	3601	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	83.6431	1746	3601	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	83.6209	2110	3601	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	83.5809	2059	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	83.5683	1918	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379885.1	s__Nonomuraea coxensis	83.559	1873	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	83.5456	1971	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_900109355.1	s__Nonomuraea pusilla	83.5014	1880	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_004348685.1	s__Nonomuraea deserti	83.4392	1866	3601	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_900111685.1	s__Nonomuraea wenchangensis	83.3926	1952	3601	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	82.9336	1751	3601	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 14:32:25,517] [INFO] GTDB search result was written to GCF_013283785.1_ASM1328378v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:25,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:25,523] [INFO] DFAST_QC result json was written to GCF_013283785.1_ASM1328378v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:25,523] [INFO] DFAST_QC completed!
[2024-01-24 14:32:25,523] [INFO] Total running time: 0h4m17s