[2024-01-24 10:47:40,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,976] [INFO] DQC Reference Directory: /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,788] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg33273fbe-2ec8-4179-91ca-d105471bdb63/GCF_004348685.1_ASM434868v1_genomic.fna.gz | prodigal -d GCF_004348685.1_ASM434868v1_genomic.fna/cds.fna -a GCF_004348685.1_ASM434868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:12,999] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:12,999] [INFO] Task started: HMMsearch
[2024-01-24 10:48:13,000] [INFO] Running command: hmmsearch --tblout GCF_004348685.1_ASM434868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/reference_markers.hmm GCF_004348685.1_ASM434868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:13,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:13,413] [INFO] Found 6/6 markers.
[2024-01-24 10:48:13,503] [INFO] Query marker FASTA was written to GCF_004348685.1_ASM434868v1_genomic.fna/markers.fasta
[2024-01-24 10:48:13,504] [INFO] Task started: Blastn
[2024-01-24 10:48:13,504] [INFO] Running command: blastn -query GCF_004348685.1_ASM434868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/reference_markers.fasta -out GCF_004348685.1_ASM434868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,813] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,817] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:14,817] [INFO] Target genome list was writen to GCF_004348685.1_ASM434868v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:14,822] [INFO] Task started: fastANI
[2024-01-24 10:48:14,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg33273fbe-2ec8-4179-91ca-d105471bdb63/GCF_004348685.1_ASM434868v1_genomic.fna.gz --refList GCF_004348685.1_ASM434868v1_genomic.fna/target_genomes.txt --output GCF_004348685.1_ASM434868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:59,111] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:59,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:59,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:59,124] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:59,124] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:48:59,125] [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 deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	100.0	3313	3343	95	inconclusive
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	95.0097	2575	3343	95	inconclusive
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	92.1426	2301	3343	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	92.0766	2505	3343	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	86.021	2011	3343	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	86.0175	2318	3343	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	86.0135	2267	3343	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	85.9332	2211	3343	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.9222	2217	3343	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.919	2187	3343	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.7647	2154	3343	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.6366	2343	3343	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.3941	1850	3343	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.2188	2148	3343	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.7487	1200	3343	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.1691	1990	3343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:59,126] [INFO] DFAST Taxonomy check result was written to GCF_004348685.1_ASM434868v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:59,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:59,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:59,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/checkm_data
[2024-01-24 10:48:59,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:59,221] [INFO] Task started: CheckM
[2024-01-24 10:48:59,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348685.1_ASM434868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348685.1_ASM434868v1_genomic.fna/checkm_input GCF_004348685.1_ASM434868v1_genomic.fna/checkm_result
[2024-01-24 10:50:26,889] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:26,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:26,916] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:26,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:26,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348685.1_ASM434868v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:26,917] [INFO] Task started: Blastn
[2024-01-24 10:50:26,917] [INFO] Running command: blastn -query GCF_004348685.1_ASM434868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf507d639-1ab4-4ec6-929e-724543e2dc06/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348685.1_ASM434868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:28,947] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:28,951] [INFO] Selected 15 target genomes.
[2024-01-24 10:50:28,951] [INFO] Target genome list was writen to GCF_004348685.1_ASM434868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:28,956] [INFO] Task started: fastANI
[2024-01-24 10:50:28,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg33273fbe-2ec8-4179-91ca-d105471bdb63/GCF_004348685.1_ASM434868v1_genomic.fna.gz --refList GCF_004348685.1_ASM434868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348685.1_ASM434868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:14,682] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:14,704] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:14,705] [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_004348685.1	s__Nonomuraea deserti	100.0	3313	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	conclusive
GCF_004348345.1	s__Nonomuraea longispora	92.1355	2302	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_014873145.1	s__Nonomuraea angiospora	86.0504	2313	3343	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	86.0035	2267	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645445.1	s__Nonomuraea cypriaca	85.9736	2020	3343	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	85.9511	2207	3343	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	85.9374	2183	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.765	2153	3343	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	85.654	2276	3343	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	85.6157	2346	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	85.5543	2111	3343	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	85.4466	2144	3343	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	85.3871	1850	3343	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	85.2289	2146	3343	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	84.2315	1972	3343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:14,707] [INFO] GTDB search result was written to GCF_004348685.1_ASM434868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:14,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:14,713] [INFO] DFAST_QC result json was written to GCF_004348685.1_ASM434868v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:14,713] [INFO] DFAST_QC completed!
[2024-01-24 10:51:14,714] [INFO] Total running time: 0h3m34s