[2023-06-30 03:13:37,378] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:13:37,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:13:37,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference
[2023-06-30 03:13:38,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:13:38,778] [INFO] Task started: Prodigal
[2023-06-30 03:13:38,778] [INFO] Running command: gunzip -c /var/lib/cwl/stg802d012c-1edc-4733-884a-5b66420d9026/GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna.gz | prodigal -d GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/cds.fna -a GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:13:46,946] [INFO] Task succeeded: Prodigal
[2023-06-30 03:13:46,946] [INFO] Task started: HMMsearch
[2023-06-30 03:13:46,946] [INFO] Running command: hmmsearch --tblout GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/reference_markers.hmm GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:13:47,218] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:13:47,219] [INFO] Found 6/6 markers.
[2023-06-30 03:13:47,252] [INFO] Query marker FASTA was written to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/markers.fasta
[2023-06-30 03:13:47,252] [INFO] Task started: Blastn
[2023-06-30 03:13:47,252] [INFO] Running command: blastn -query GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/markers.fasta -db /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/reference_markers.fasta -out GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:13:48,552] [INFO] Task succeeded: Blastn
[2023-06-30 03:13:48,556] [INFO] Selected 38 target genomes.
[2023-06-30 03:13:48,557] [INFO] Target genome list was writen to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/target_genomes.txt
[2023-06-30 03:13:48,558] [INFO] Task started: fastANI
[2023-06-30 03:13:48,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg802d012c-1edc-4733-884a-5b66420d9026/GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna.gz --refList GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/target_genomes.txt --output GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:14:25,723] [INFO] Task succeeded: fastANI
[2023-06-30 03:14:25,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:14:25,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:14:25,764] [INFO] Found 38 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:14:25,765] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:14:25,765] [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
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	77.2234	114	753	95	below_threshold
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	77.0819	88	753	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	77.0594	98	753	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	76.9938	122	753	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.9416	127	753	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	76.9233	117	753	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	76.9186	142	753	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	76.8978	128	753	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.8614	106	753	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	76.8351	150	753	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	76.8175	125	753	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	76.8146	128	753	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.7935	113	753	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	76.732	124	753	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	76.6697	137	753	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	76.6256	143	753	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	76.6213	93	753	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	76.607	110	753	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	76.5984	143	753	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	76.5912	113	753	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	76.5708	107	753	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.5687	127	753	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	76.5502	107	753	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	76.5368	119	753	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	76.5284	129	753	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	76.5241	96	753	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	76.5073	129	753	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	76.421	121	753	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	76.4197	128	753	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.3649	92	753	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	76.3575	113	753	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	76.3254	122	753	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	76.2313	131	753	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	76.2154	111	753	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	76.2106	110	753	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	76.1466	127	753	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	76.1447	127	753	95	below_threshold
Amycolatopsis mediterranei	strain=S699	GCA_000220945.1	33910	33910	type	True	75.9038	128	753	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:14:25,771] [INFO] DFAST Taxonomy check result was written to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/tc_result.tsv
[2023-06-30 03:14:25,772] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:14:25,772] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:14:25,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/checkm_data
[2023-06-30 03:14:25,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:14:25,811] [INFO] Task started: CheckM
[2023-06-30 03:14:25,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/checkm_input GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/checkm_result
[2023-06-30 03:14:55,389] [INFO] Task succeeded: CheckM
[2023-06-30 03:14:55,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 03:14:55,414] [INFO] ===== Completeness check finished =====
[2023-06-30 03:14:55,414] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:14:55,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/markers.fasta)
[2023-06-30 03:14:55,415] [INFO] Task started: Blastn
[2023-06-30 03:14:55,415] [INFO] Running command: blastn -query GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/markers.fasta -db /var/lib/cwl/stgad985de6-3192-44ae-bad5-12de028192f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:14:57,480] [INFO] Task succeeded: Blastn
[2023-06-30 03:14:57,485] [INFO] Selected 8 target genomes.
[2023-06-30 03:14:57,485] [INFO] Target genome list was writen to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:14:57,487] [INFO] Task started: fastANI
[2023-06-30 03:14:57,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg802d012c-1edc-4733-884a-5b66420d9026/GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna.gz --refList GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/target_genomes_gtdb.txt --output GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:15:02,115] [INFO] Task succeeded: fastANI
[2023-06-30 03:15:02,129] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:15:02,129] [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
GCA_903940375.1	s__UBA10649 sp903940375	100.0	740	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	conclusive
GCA_903908025.1	s__UBA10649 sp903908025	85.5336	511	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.87	97.91	0.84	0.77	3	-
GCA_016717115.1	s__UBA10649 sp016717115	79.9012	360	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	79.0818	325	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856385.1	s__UBA10649 sp017856385	78.9792	263	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849335.1	s__UBA10649 sp017849335	78.4613	232	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456155.1	s__UBA10649 sp003456155	78.407	219	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699015.1	s__WLND01 sp009699015	77.7666	203	753	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:15:02,131] [INFO] GTDB search result was written to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/result_gtdb.tsv
[2023-06-30 03:15:02,132] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:15:02,138] [INFO] DFAST_QC result json was written to GCA_903940375.1_freshwater_MAG_---_Loc090907-6m_bin-560_genomic.fna/dqc_result.json
[2023-06-30 03:15:02,138] [INFO] DFAST_QC completed!
[2023-06-30 03:15:02,138] [INFO] Total running time: 0h1m25s