[2024-01-24 15:01:23,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference
[2024-01-24 15:01:24,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,696] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg358447d6-60ce-45e8-a3e6-2ec7f521d124/GCF_025996515.1_ASM2599651v1_genomic.fna.gz | prodigal -d GCF_025996515.1_ASM2599651v1_genomic.fna/cds.fna -a GCF_025996515.1_ASM2599651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:49,972] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:49,972] [INFO] Task started: HMMsearch
[2024-01-24 15:01:49,972] [INFO] Running command: hmmsearch --tblout GCF_025996515.1_ASM2599651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/reference_markers.hmm GCF_025996515.1_ASM2599651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:50,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:50,494] [INFO] Found 6/6 markers.
[2024-01-24 15:01:50,563] [INFO] Query marker FASTA was written to GCF_025996515.1_ASM2599651v1_genomic.fna/markers.fasta
[2024-01-24 15:01:50,563] [INFO] Task started: Blastn
[2024-01-24 15:01:50,564] [INFO] Running command: blastn -query GCF_025996515.1_ASM2599651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/reference_markers.fasta -out GCF_025996515.1_ASM2599651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:52,002] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:52,007] [INFO] Selected 31 target genomes.
[2024-01-24 15:01:52,008] [INFO] Target genome list was writen to GCF_025996515.1_ASM2599651v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:52,458] [INFO] Task started: fastANI
[2024-01-24 15:01:52,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg358447d6-60ce-45e8-a3e6-2ec7f521d124/GCF_025996515.1_ASM2599651v1_genomic.fna.gz --refList GCF_025996515.1_ASM2599651v1_genomic.fna/target_genomes.txt --output GCF_025996515.1_ASM2599651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:44,091] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:44,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:44,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:44,123] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:44,123] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:44,124] [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
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	78.7337	1069	2761	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	78.6874	1009	2761	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	78.6477	964	2761	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	78.5939	900	2761	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	78.5053	962	2761	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	78.4881	870	2761	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	78.4611	988	2761	95	below_threshold
Streptosporangium saharense	strain=CECT 8840	GCA_014203715.1	1706840	1706840	type	True	78.4577	915	2761	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	78.4545	948	2761	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	78.3912	903	2761	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	78.3611	983	2761	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	78.3033	901	2761	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	78.2737	902	2761	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	78.2565	923	2761	95	below_threshold
Spongiactinospora rosea	strain=LHW63015	GCA_003315795.1	2248750	2248750	type	True	78.2147	925	2761	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	78.2105	832	2761	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	78.1809	908	2761	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	78.1332	903	2761	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	78.116	968	2761	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	78.0999	778	2761	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	78.0049	954	2761	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	77.9936	994	2761	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	77.9737	803	2761	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	77.9704	909	2761	95	below_threshold
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	77.9423	800	2761	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	77.935	812	2761	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	77.8748	891	2761	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	77.8194	860	2761	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.9432	796	2761	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.8669	803	2761	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	76.7096	749	2761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:44,126] [INFO] DFAST Taxonomy check result was written to GCF_025996515.1_ASM2599651v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:44,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:44,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:44,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/checkm_data
[2024-01-24 15:02:44,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:44,222] [INFO] Task started: CheckM
[2024-01-24 15:02:44,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025996515.1_ASM2599651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025996515.1_ASM2599651v1_genomic.fna/checkm_input GCF_025996515.1_ASM2599651v1_genomic.fna/checkm_result
[2024-01-24 15:04:00,000] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:00,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.09%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,032] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:00,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:00,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025996515.1_ASM2599651v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:00,033] [INFO] Task started: Blastn
[2024-01-24 15:04:00,034] [INFO] Running command: blastn -query GCF_025996515.1_ASM2599651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg701e2bac-6636-43d0-b7a5-f2e8257857ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_025996515.1_ASM2599651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:02,195] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:02,199] [INFO] Selected 30 target genomes.
[2024-01-24 15:04:02,200] [INFO] Target genome list was writen to GCF_025996515.1_ASM2599651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:02,245] [INFO] Task started: fastANI
[2024-01-24 15:04:02,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg358447d6-60ce-45e8-a3e6-2ec7f521d124/GCF_025996515.1_ASM2599651v1_genomic.fna.gz --refList GCF_025996515.1_ASM2599651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025996515.1_ASM2599651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:56,099] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:56,122] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:04:56,123] [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_016863435.1	s__Sinosporangium siamense	78.7679	889	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	78.7582	1064	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	78.6797	1007	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_002149035.1	s__Streptosporangium minutum	78.6353	964	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	78.6255	972	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	78.6026	921	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_001528665.1	s__Microtetraspora malaysiensis	78.5735	904	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	78.4881	967	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014203715.1	s__Streptosporangium saharense	78.4745	911	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	78.4672	874	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	78.4633	944	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_016863135.1	s__Planobispora longispora	78.4573	991	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	78.3892	975	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	78.3701	907	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	78.3076	899	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001570405.1	s__Microtetraspora niveoalba	78.2498	909	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315795.1	s__Desertactinospora sp003315795	78.2273	921	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Desertactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	78.215	942	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862995.1	s__Acrocarpospora phusangensis	78.1843	838	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687845.1	s__Acrocarpospora corrugata	78.1277	850	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242605.1	s__Thermopolyspora sp003242605	78.041	669	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	78.0359	1062	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	78.0305	771	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	77.9776	998	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594875.1	s__Bailinhaonella thermotolerans	77.9704	931	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874465.1	s__Microbispora bryophytorum	77.9626	805	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_006874475.1	s__Microbispora hainanensis	77.8048	863	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_001552635.1	s__Spirillospora hibisca	77.1061	750	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552175.1	s__Spirillospora kijaniata	76.993	842	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_005405885.1	s__Gandjariella thermophila	75.975	422	2761	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:56,124] [INFO] GTDB search result was written to GCF_025996515.1_ASM2599651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:56,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:56,130] [INFO] DFAST_QC result json was written to GCF_025996515.1_ASM2599651v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:56,131] [INFO] DFAST_QC completed!
[2024-01-24 15:04:56,131] [INFO] Total running time: 0h3m33s