[2024-01-24 13:57:16,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference
[2024-01-24 13:57:17,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,797] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,797] [INFO] Running command: gunzip -c /var/lib/cwl/stg42a80039-db8e-45fa-995b-49c26fe644d9/GCF_000015025.1_ASM1502v1_genomic.fna.gz | prodigal -d GCF_000015025.1_ASM1502v1_genomic.fna/cds.fna -a GCF_000015025.1_ASM1502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:25,506] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:25,506] [INFO] Task started: HMMsearch
[2024-01-24 13:57:25,506] [INFO] Running command: hmmsearch --tblout GCF_000015025.1_ASM1502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/reference_markers.hmm GCF_000015025.1_ASM1502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:25,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:25,747] [INFO] Found 6/6 markers.
[2024-01-24 13:57:25,770] [INFO] Query marker FASTA was written to GCF_000015025.1_ASM1502v1_genomic.fna/markers.fasta
[2024-01-24 13:57:25,770] [INFO] Task started: Blastn
[2024-01-24 13:57:25,770] [INFO] Running command: blastn -query GCF_000015025.1_ASM1502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/reference_markers.fasta -out GCF_000015025.1_ASM1502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:26,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:26,567] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:26,567] [INFO] Target genome list was writen to GCF_000015025.1_ASM1502v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:26,576] [INFO] Task started: fastANI
[2024-01-24 13:57:26,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg42a80039-db8e-45fa-995b-49c26fe644d9/GCF_000015025.1_ASM1502v1_genomic.fna.gz --refList GCF_000015025.1_ASM1502v1_genomic.fna/target_genomes.txt --output GCF_000015025.1_ASM1502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:52,520] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:52,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:52,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:52,540] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:52,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:52,540] [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
Acidothermus cellulolyticus	strain=11B; ATCC 43068	GCA_000015025.1	28049	28049	type	True	100.0	814	814	95	conclusive
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.3764	85	814	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	76.301	138	814	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	76.2873	92	814	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	76.1776	135	814	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	76.0728	98	814	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	76.066	112	814	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	75.9958	70	814	95	below_threshold
Tenggerimyces flavus	strain=DSM 28944	GCA_016907715.1	1708749	1708749	type	True	75.9949	110	814	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	75.9252	83	814	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	75.9057	102	814	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	75.8961	133	814	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	75.888	125	814	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	75.842	68	814	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	75.8304	115	814	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	75.8293	106	814	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	75.8227	132	814	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	75.8152	121	814	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	75.7938	140	814	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	75.7571	80	814	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	75.7134	130	814	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	75.7056	50	814	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.6727	168	814	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	75.6411	122	814	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	75.6365	84	814	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	75.5699	79	814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,542] [INFO] DFAST Taxonomy check result was written to GCF_000015025.1_ASM1502v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:52,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:52,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:52,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/checkm_data
[2024-01-24 13:57:52,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:52,569] [INFO] Task started: CheckM
[2024-01-24 13:57:52,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015025.1_ASM1502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015025.1_ASM1502v1_genomic.fna/checkm_input GCF_000015025.1_ASM1502v1_genomic.fna/checkm_result
[2024-01-24 13:58:21,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:21,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,090] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:21,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:21,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015025.1_ASM1502v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:21,092] [INFO] Task started: Blastn
[2024-01-24 13:58:21,092] [INFO] Running command: blastn -query GCF_000015025.1_ASM1502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85532a3e-8173-46db-8cd4-a61d196cd837/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015025.1_ASM1502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,234] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:22,234] [INFO] Target genome list was writen to GCF_000015025.1_ASM1502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:22,267] [INFO] Task started: fastANI
[2024-01-24 13:58:22,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg42a80039-db8e-45fa-995b-49c26fe644d9/GCF_000015025.1_ASM1502v1_genomic.fna.gz --refList GCF_000015025.1_ASM1502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015025.1_ASM1502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:46,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:46,503] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:46,503] [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_000015025.1	s__Acidothermus cellulolyticus	100.0	814	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Acidothermales;f__Acidothermaceae;g__Acidothermus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_011299595.1	s__Marmoricola_A sp011299595	76.591	86	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134755.1	s__PALSA-607 sp003134755	76.3171	112	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Acidothermales;f__Acidothermaceae;g__PALSA-607	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205275.1	s__Sphaerisporangium siamense	76.3156	137	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014200435.1	s__Sphaerisporangium krabiense	76.2646	137	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003432485.1	s__Spirillospora sp003432485	76.1529	113	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813405.1	s__Streptomyces sp002813405	76.0979	112	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570425.1	s__Blastococcus sp004570425	76.0503	98	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100605.1	s__Sinosporangium album	75.9156	90	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751605.1	s__Kitasatospora cineracea	75.9141	160	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.58	96.37	0.89	0.86	4	-
GCF_002754615.1	s__Kitasatospora sp002754615	75.9112	149	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003075095.1	s__Blastococcus litoris	75.9057	102	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	75.888	125	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	75.8293	106	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	75.8152	121	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426185.1	s__Cellulomonas sp000426185	75.8116	69	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672815.1	s__Mycobacterium sp001672815	75.7046	63	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	75.6413	131	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_000426525.1	s__Nocardioides alkalitolerans	75.6365	84	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044995.1	s__Streptomyces mesophilus	75.5762	102	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.86	0.86	2	-
GCF_014649115.1	s__Streptomyces eurythermus	75.5112	135	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCA_003164955.1	s__Bog-532 sp003164955	75.3698	95	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	99.74	99.72	0.91	0.90	3	-
GCA_012514545.1	s__Actinotalea sp012514545	75.3498	73	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,505] [INFO] GTDB search result was written to GCF_000015025.1_ASM1502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:46,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:46,511] [INFO] DFAST_QC result json was written to GCF_000015025.1_ASM1502v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:46,512] [INFO] DFAST_QC completed!
[2024-01-24 13:58:46,512] [INFO] Total running time: 0h1m30s