[2024-01-24 13:46:18,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference
[2024-01-24 13:46:20,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:20,055] [INFO] Task started: Prodigal
[2024-01-24 13:46:20,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe0a201b-06c1-4c44-bda4-3f8cbd804d19/GCF_014648435.1_ASM1464843v1_genomic.fna.gz | prodigal -d GCF_014648435.1_ASM1464843v1_genomic.fna/cds.fna -a GCF_014648435.1_ASM1464843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:56,548] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:56,548] [INFO] Task started: HMMsearch
[2024-01-24 13:46:56,548] [INFO] Running command: hmmsearch --tblout GCF_014648435.1_ASM1464843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/reference_markers.hmm GCF_014648435.1_ASM1464843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:57,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:57,114] [INFO] Found 6/6 markers.
[2024-01-24 13:46:57,220] [INFO] Query marker FASTA was written to GCF_014648435.1_ASM1464843v1_genomic.fna/markers.fasta
[2024-01-24 13:46:57,221] [INFO] Task started: Blastn
[2024-01-24 13:46:57,221] [INFO] Running command: blastn -query GCF_014648435.1_ASM1464843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/reference_markers.fasta -out GCF_014648435.1_ASM1464843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,693] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:58,693] [INFO] Target genome list was writen to GCF_014648435.1_ASM1464843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:58,740] [INFO] Task started: fastANI
[2024-01-24 13:46:58,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe0a201b-06c1-4c44-bda4-3f8cbd804d19/GCF_014648435.1_ASM1464843v1_genomic.fna.gz --refList GCF_014648435.1_ASM1464843v1_genomic.fna/target_genomes.txt --output GCF_014648435.1_ASM1464843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:00,705] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:00,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:00,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:00,725] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:00,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:00,725] [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 spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	100.0	3768	3776	95	conclusive
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	84.7333	2309	3776	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	84.6805	2188	3776	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	84.5397	2333	3776	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	84.5293	2336	3776	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	84.4327	2158	3776	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	84.3986	2103	3776	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	84.3796	2370	3776	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	84.3474	2141	3776	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	84.3366	1978	3776	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	84.2699	2299	3776	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	84.1966	2141	3776	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	84.1897	2137	3776	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	84.164	1979	3776	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	84.0423	2173	3776	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	84.0397	2118	3776	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	84.0385	1757	3776	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	83.9216	1938	3776	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.905	1260	3776	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.3592	1758	3776	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.0063	2096	3776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:00,727] [INFO] DFAST Taxonomy check result was written to GCF_014648435.1_ASM1464843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:00,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:00,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:00,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/checkm_data
[2024-01-24 13:48:00,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:00,827] [INFO] Task started: CheckM
[2024-01-24 13:48:00,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648435.1_ASM1464843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648435.1_ASM1464843v1_genomic.fna/checkm_input GCF_014648435.1_ASM1464843v1_genomic.fna/checkm_result
[2024-01-24 13:49:57,245] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:57,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 62.50%
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,281] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:57,282] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:57,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648435.1_ASM1464843v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:57,282] [INFO] Task started: Blastn
[2024-01-24 13:49:57,282] [INFO] Running command: blastn -query GCF_014648435.1_ASM1464843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg882dcc76-bd74-48ea-bad9-f07df9818e0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648435.1_ASM1464843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:59,587] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:59,592] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:59,592] [INFO] Target genome list was writen to GCF_014648435.1_ASM1464843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:59,625] [INFO] Task started: fastANI
[2024-01-24 13:49:59,626] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe0a201b-06c1-4c44-bda4-3f8cbd804d19/GCF_014648435.1_ASM1464843v1_genomic.fna.gz --refList GCF_014648435.1_ASM1464843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648435.1_ASM1464843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:48,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:49,009] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:49,009] [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_014648435.1	s__Nonomuraea spiralis	100.0	3768	3776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	conclusive
GCA_013362835.1	s__Nonomuraea sp013362835	90.316	1002	3776	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	84.7598	2303	3776	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	84.6479	2195	3776	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	84.5244	2337	3776	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	84.4998	2341	3776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	84.4173	2098	3776	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	84.3817	2371	3776	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	84.3621	2138	3776	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	84.3345	1979	3776	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	84.2657	2298	3776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	84.174	1978	3776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_008086045.1	s__Nonomuraea sp008086045	84.1355	2352	3776	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	84.1145	2145	3776	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	84.0253	2178	3776	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	84.0227	2122	3776	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 13:50:49,012] [INFO] GTDB search result was written to GCF_014648435.1_ASM1464843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:49,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:49,016] [INFO] DFAST_QC result json was written to GCF_014648435.1_ASM1464843v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:49,016] [INFO] DFAST_QC completed!
[2024-01-24 13:50:49,016] [INFO] Total running time: 0h4m30s