[2024-01-24 14:30:47,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference
[2024-01-24 14:30:48,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,473] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3d62a94-9f4b-4e78-83bd-341366257797/GCF_014647775.1_ASM1464777v1_genomic.fna.gz | prodigal -d GCF_014647775.1_ASM1464777v1_genomic.fna/cds.fna -a GCF_014647775.1_ASM1464777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:04,983] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:04,984] [INFO] Task started: HMMsearch
[2024-01-24 14:31:04,984] [INFO] Running command: hmmsearch --tblout GCF_014647775.1_ASM1464777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/reference_markers.hmm GCF_014647775.1_ASM1464777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:05,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:05,319] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf3d62a94-9f4b-4e78-83bd-341366257797/GCF_014647775.1_ASM1464777v1_genomic.fna.gz]
[2024-01-24 14:31:05,370] [INFO] Query marker FASTA was written to GCF_014647775.1_ASM1464777v1_genomic.fna/markers.fasta
[2024-01-24 14:31:05,371] [INFO] Task started: Blastn
[2024-01-24 14:31:05,371] [INFO] Running command: blastn -query GCF_014647775.1_ASM1464777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/reference_markers.fasta -out GCF_014647775.1_ASM1464777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:06,585] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:06,589] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:06,589] [INFO] Target genome list was writen to GCF_014647775.1_ASM1464777v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:06,597] [INFO] Task started: fastANI
[2024-01-24 14:31:06,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d62a94-9f4b-4e78-83bd-341366257797/GCF_014647775.1_ASM1464777v1_genomic.fna.gz --refList GCF_014647775.1_ASM1464777v1_genomic.fna/target_genomes.txt --output GCF_014647775.1_ASM1464777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:35,839] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:35,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:35,854] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:35,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:35,854] [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
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	100.0	1902	1905	95	conclusive
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	99.9865	1902	1905	95	conclusive
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	79.9729	1004	1905	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	79.9039	984	1905	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	79.6723	1017	1905	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	79.6476	980	1905	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	79.6211	955	1905	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	79.617	974	1905	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	79.596	978	1905	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	79.5591	984	1905	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	79.5572	793	1905	95	below_threshold
Microtetraspora fusca	strain=NBRC 13915	GCA_001570365.1	1997	1997	type	True	79.5183	979	1905	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.5052	1036	1905	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	79.4126	918	1905	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.3697	704	1905	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.3308	910	1905	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.7403	999	1905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,856] [INFO] DFAST Taxonomy check result was written to GCF_014647775.1_ASM1464777v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:35,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:35,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:35,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/checkm_data
[2024-01-24 14:31:35,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:35,916] [INFO] Task started: CheckM
[2024-01-24 14:31:35,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647775.1_ASM1464777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647775.1_ASM1464777v1_genomic.fna/checkm_input GCF_014647775.1_ASM1464777v1_genomic.fna/checkm_result
[2024-01-24 14:32:36,588] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:36,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:36,611] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:36,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:36,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647775.1_ASM1464777v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:36,612] [INFO] Task started: Blastn
[2024-01-24 14:32:36,612] [INFO] Running command: blastn -query GCF_014647775.1_ASM1464777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f45fd47-0a87-4c66-8311-3ae965183cc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647775.1_ASM1464777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:38,361] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:38,365] [INFO] Selected 16 target genomes.
[2024-01-24 14:32:38,366] [INFO] Target genome list was writen to GCF_014647775.1_ASM1464777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:38,380] [INFO] Task started: fastANI
[2024-01-24 14:32:38,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d62a94-9f4b-4e78-83bd-341366257797/GCF_014647775.1_ASM1464777v1_genomic.fna.gz --refList GCF_014647775.1_ASM1464777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647775.1_ASM1464777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:05,173] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:05,199] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:05,199] [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_006716785.1	s__Thermopolyspora flexuosa	99.9865	1902	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_003242605.1	s__Thermopolyspora sp003242605	93.2043	1385	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092645.1	s__Thermobispora bispora	80.7373	870	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobispora	95.0	99.72	99.67	0.98	0.98	4	-
GCF_016863395.1	s__Sphaerisporangium rufum	79.8734	989	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	79.7404	983	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863035.1	s__Microbispora corallina	79.6942	1011	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCA_003260025.2	s__Microbispora triticiradicis	79.647	924	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_014200435.1	s__Sphaerisporangium krabiense	79.6405	980	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016863175.1	s__Planobispora siamensis	79.6178	1038	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_001570405.1	s__Microtetraspora niveoalba	79.5975	979	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863115.1	s__Sphaerimonospora thailandensis	79.5746	791	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205275.1	s__Sphaerisporangium siamense	79.5581	985	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001570365.1	s__Microtetraspora fusca	79.5456	974	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863015.1	s__Microbispora amethystogenes	79.5427	971	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_000379885.1	s__Nonomuraea coxensis	79.4196	1042	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	79.4038	923	1905	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:05,201] [INFO] GTDB search result was written to GCF_014647775.1_ASM1464777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:05,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:05,206] [INFO] DFAST_QC result json was written to GCF_014647775.1_ASM1464777v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:05,206] [INFO] DFAST_QC completed!
[2024-01-24 14:33:05,207] [INFO] Total running time: 0h2m18s