[2024-01-24 12:37:24,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference
[2024-01-24 12:37:25,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,597] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,597] [INFO] Running command: gunzip -c /var/lib/cwl/stgaca5b5ea-e21b-4fa6-8120-a59e6c485684/GCF_021502675.1_ASM2150267v1_genomic.fna.gz | prodigal -d GCF_021502675.1_ASM2150267v1_genomic.fna/cds.fna -a GCF_021502675.1_ASM2150267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:52,975] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:52,975] [INFO] Task started: HMMsearch
[2024-01-24 12:37:52,976] [INFO] Running command: hmmsearch --tblout GCF_021502675.1_ASM2150267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/reference_markers.hmm GCF_021502675.1_ASM2150267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:53,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:53,350] [INFO] Found 6/6 markers.
[2024-01-24 12:37:53,426] [INFO] Query marker FASTA was written to GCF_021502675.1_ASM2150267v1_genomic.fna/markers.fasta
[2024-01-24 12:37:53,426] [INFO] Task started: Blastn
[2024-01-24 12:37:53,427] [INFO] Running command: blastn -query GCF_021502675.1_ASM2150267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/reference_markers.fasta -out GCF_021502675.1_ASM2150267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:54,911] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:54,915] [INFO] Selected 32 target genomes.
[2024-01-24 12:37:54,916] [INFO] Target genome list was writen to GCF_021502675.1_ASM2150267v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:54,939] [INFO] Task started: fastANI
[2024-01-24 12:37:54,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5b5ea-e21b-4fa6-8120-a59e6c485684/GCF_021502675.1_ASM2150267v1_genomic.fna.gz --refList GCF_021502675.1_ASM2150267v1_genomic.fna/target_genomes.txt --output GCF_021502675.1_ASM2150267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:47,097] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:47,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:47,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:47,129] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:38:47,129] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:38:47,130] [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
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	79.7186	1356	3191	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	79.6751	1379	3191	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	78.2655	886	3191	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	78.1604	800	3191	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	78.1593	782	3191	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	78.0307	1046	3191	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	77.9647	891	3191	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	77.9608	856	3191	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	77.911	1023	3191	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	77.8875	1089	3191	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	77.855	1107	3191	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	77.8248	831	3191	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	77.823	884	3191	95	below_threshold
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	77.8148	805	3191	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	77.759	1030	3191	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	77.7584	907	3191	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	77.7548	877	3191	95	below_threshold
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	77.7521	969	3191	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	77.7319	1030	3191	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	77.703	860	3191	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	77.6983	1029	3191	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	77.6414	968	3191	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	77.6278	833	3191	95	below_threshold
Streptomyces coryli	strain=A7024	GCA_011044975.1	1128680	1128680	type	True	77.5442	924	3191	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	77.5116	963	3191	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	77.193	800	3191	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	77.0316	858	3191	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	76.9502	526	3191	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	76.5792	754	3191	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.3815	1073	3191	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	76.2594	938	3191	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	75.9748	304	3191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:47,191] [INFO] DFAST Taxonomy check result was written to GCF_021502675.1_ASM2150267v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:47,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:47,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:47,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/checkm_data
[2024-01-24 12:38:47,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:47,281] [INFO] Task started: CheckM
[2024-01-24 12:38:47,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021502675.1_ASM2150267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021502675.1_ASM2150267v1_genomic.fna/checkm_input GCF_021502675.1_ASM2150267v1_genomic.fna/checkm_result
[2024-01-24 12:41:09,506] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:09,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:09,533] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:09,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:09,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021502675.1_ASM2150267v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:09,534] [INFO] Task started: Blastn
[2024-01-24 12:41:09,534] [INFO] Running command: blastn -query GCF_021502675.1_ASM2150267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03a3a6-7efa-4bb3-b478-849f8dc71dad/dqc_reference/reference_markers_gtdb.fasta -out GCF_021502675.1_ASM2150267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:11,967] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:11,971] [INFO] Selected 28 target genomes.
[2024-01-24 12:41:11,971] [INFO] Target genome list was writen to GCF_021502675.1_ASM2150267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:12,003] [INFO] Task started: fastANI
[2024-01-24 12:41:12,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5b5ea-e21b-4fa6-8120-a59e6c485684/GCF_021502675.1_ASM2150267v1_genomic.fna.gz --refList GCF_021502675.1_ASM2150267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021502675.1_ASM2150267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:58,445] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:58,475] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:58,476] [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_002024165.1	s__Embleya scabrispora_A	79.7244	1393	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372745.1	s__Embleya scabrispora	79.6845	1368	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003967355.1	s__Embleya hyalina	79.6659	1380	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144095.1	s__Streptomyces sp003144095	78.4288	856	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715685.1	s__Streptomyces lilacinus	78.2749	877	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999245.1	s__Streptomyces sp015999245	77.9958	851	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596465.1	s__Kitasatospora sp014596465	77.9932	1021	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625365.1	s__Kitasatospora sp001625365	77.9281	1070	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656195.1	s__Kitasatospora xanthocidica	77.9036	1107	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418575.1	s__Streptomyces_D griseoplanus	77.8367	798	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650475.1	s__Streptomyces albogriseolus	77.8214	905	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCA_014656175.1	s__Streptomyces werraensis	77.779	907	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187435.1	s__Streptomyces caatingaensis	77.7762	897	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950035.1	s__Streptomyces sp000158895	77.754	1018	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.52	95.50	0.87	0.87	3	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	77.7393	1028	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	77.7358	882	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651135.1	s__Streptomyces echinoruber	77.7302	913	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008634025.1	s__Streptomyces albofaciens	77.7152	1043	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787855.1	s__Streptacidiphilus anmyonensis	77.7126	983	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044975.1	s__Streptomyces sp011044975	77.5075	938	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	77.1182	774	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	76.9942	874	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	76.951	526	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	76.5767	756	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	76.3478	804	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648495.1	s__Spirillospora cremea	76.2584	938	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553565.1	s__Actinomyces radicidentis	75.9565	308	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	75.9099	674	3191	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:58,477] [INFO] GTDB search result was written to GCF_021502675.1_ASM2150267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:58,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:58,483] [INFO] DFAST_QC result json was written to GCF_021502675.1_ASM2150267v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:58,483] [INFO] DFAST_QC completed!
[2024-01-24 12:41:58,483] [INFO] Total running time: 0h4m34s