[2023-06-07 22:49:22,668] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:49:22,671] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:49:22,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference
[2023-06-07 22:49:25,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:49:25,114] [INFO] Task started: Prodigal
[2023-06-07 22:49:25,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg30943bff-9e5e-4f91-a184-62530088b800/GCA_945861925.1_MaH-09apr19-236_genomic.fna.gz | prodigal -d GCA_945861925.1_MaH-09apr19-236_genomic.fna/cds.fna -a GCA_945861925.1_MaH-09apr19-236_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:49:35,259] [INFO] Task succeeded: Prodigal
[2023-06-07 22:49:35,259] [INFO] Task started: HMMsearch
[2023-06-07 22:49:35,259] [INFO] Running command: hmmsearch --tblout GCA_945861925.1_MaH-09apr19-236_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/reference_markers.hmm GCA_945861925.1_MaH-09apr19-236_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:49:35,536] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:49:35,537] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg30943bff-9e5e-4f91-a184-62530088b800/GCA_945861925.1_MaH-09apr19-236_genomic.fna.gz]
[2023-06-07 22:49:35,574] [INFO] Query marker FASTA was written to GCA_945861925.1_MaH-09apr19-236_genomic.fna/markers.fasta
[2023-06-07 22:49:35,574] [INFO] Task started: Blastn
[2023-06-07 22:49:35,574] [INFO] Running command: blastn -query GCA_945861925.1_MaH-09apr19-236_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/reference_markers.fasta -out GCA_945861925.1_MaH-09apr19-236_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:49:36,554] [INFO] Task succeeded: Blastn
[2023-06-07 22:49:36,559] [INFO] Selected 29 target genomes.
[2023-06-07 22:49:36,559] [INFO] Target genome list was writen to GCA_945861925.1_MaH-09apr19-236_genomic.fna/target_genomes.txt
[2023-06-07 22:49:36,567] [INFO] Task started: fastANI
[2023-06-07 22:49:36,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg30943bff-9e5e-4f91-a184-62530088b800/GCA_945861925.1_MaH-09apr19-236_genomic.fna.gz --refList GCA_945861925.1_MaH-09apr19-236_genomic.fna/target_genomes.txt --output GCA_945861925.1_MaH-09apr19-236_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:49:58,100] [INFO] Task succeeded: fastANI
[2023-06-07 22:49:58,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:49:58,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:49:58,124] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:49:58,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:49:58,125] [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
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.4014	72	1069	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	76.3085	70	1069	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	76.1913	73	1069	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	76.1122	84	1069	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.0688	85	1069	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	76.0614	84	1069	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	76.0549	103	1069	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	76.0474	83	1069	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	75.9968	79	1069	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	75.9929	107	1069	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	75.9679	79	1069	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	75.951	104	1069	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	75.9196	103	1069	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	75.9124	119	1069	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	75.9012	120	1069	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	75.703	58	1069	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	75.6642	60	1069	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	75.6246	78	1069	95	below_threshold
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	75.6243	78	1069	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	75.6097	69	1069	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	75.6082	51	1069	95	below_threshold
Actinophytocola algeriensis	strain=CECT 8960	GCA_014203735.1	1768010	1768010	type	True	75.5841	78	1069	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	75.5835	53	1069	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	75.5625	53	1069	95	below_threshold
Amycolatopsis xylanica	strain=CPCC 202699	GCA_900107045.1	589385	589385	type	True	75.509	85	1069	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	75.495	61	1069	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	75.4405	67	1069	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:49:58,126] [INFO] DFAST Taxonomy check result was written to GCA_945861925.1_MaH-09apr19-236_genomic.fna/tc_result.tsv
[2023-06-07 22:49:58,127] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:49:58,127] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:49:58,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/checkm_data
[2023-06-07 22:49:58,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:49:58,165] [INFO] Task started: CheckM
[2023-06-07 22:49:58,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861925.1_MaH-09apr19-236_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861925.1_MaH-09apr19-236_genomic.fna/checkm_input GCA_945861925.1_MaH-09apr19-236_genomic.fna/checkm_result
[2023-06-07 22:50:31,312] [INFO] Task succeeded: CheckM
[2023-06-07 22:50:31,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.31%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:50:31,335] [INFO] ===== Completeness check finished =====
[2023-06-07 22:50:31,336] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:50:31,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861925.1_MaH-09apr19-236_genomic.fna/markers.fasta)
[2023-06-07 22:50:31,337] [INFO] Task started: Blastn
[2023-06-07 22:50:31,337] [INFO] Running command: blastn -query GCA_945861925.1_MaH-09apr19-236_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49c5325-bf03-40fd-99f7-9d935bfba9c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861925.1_MaH-09apr19-236_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:50:32,624] [INFO] Task succeeded: Blastn
[2023-06-07 22:50:32,628] [INFO] Selected 20 target genomes.
[2023-06-07 22:50:32,629] [INFO] Target genome list was writen to GCA_945861925.1_MaH-09apr19-236_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:50:32,764] [INFO] Task started: fastANI
[2023-06-07 22:50:32,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg30943bff-9e5e-4f91-a184-62530088b800/GCA_945861925.1_MaH-09apr19-236_genomic.fna.gz --refList GCA_945861925.1_MaH-09apr19-236_genomic.fna/target_genomes_gtdb.txt --output GCA_945861925.1_MaH-09apr19-236_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:50:47,039] [INFO] Task succeeded: fastANI
[2023-06-07 22:50:47,055] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 22:50:47,056] [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_009699015.1	s__WLND01 sp009699015	85.2986	634	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
GCA_009726075.1	s__WLND01 sp009726075	78.9959	242	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970025.1	s__REEB460 sp018970025	77.4208	157	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__REEB460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908025.1	s__UBA10649 sp903908025	77.3511	172	1069	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_903940375.1	s__UBA10649 sp903940375	77.3222	153	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	-
GCA_016125355.1	s__UBA10649 sp016125355	77.1733	168	1069	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_016717115.1	s__UBA10649 sp016717115	77.1538	200	1069	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	76.8838	174	1069	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_004379115.1	s__Mxb001 sp004379115	76.8701	91	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848435.1	s__Mxb001 sp903848435	76.8542	78	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	-
GCA_017849335.1	s__UBA10649 sp017849335	76.8288	115	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594885.1	s__Vallicoccus soli	76.2759	106	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848795.1	s__JAFIHG01 sp017848795	76.2586	83	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__JAFIHG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286695.1	s__Streptomyces albireticuli	75.9496	100	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	75.9417	88	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312005.1	s__Cellulomonas massiliensis	75.8201	56	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014836755.1	s__Oerskovia sp014836755	75.703	58	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	75.6866	92	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	75.5879	88	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946865.1	s__Antribacter gilvus	75.3792	58	1069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Antribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 22:50:47,058] [INFO] GTDB search result was written to GCA_945861925.1_MaH-09apr19-236_genomic.fna/result_gtdb.tsv
[2023-06-07 22:50:47,058] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:50:47,063] [INFO] DFAST_QC result json was written to GCA_945861925.1_MaH-09apr19-236_genomic.fna/dqc_result.json
[2023-06-07 22:50:47,064] [INFO] DFAST_QC completed!
[2023-06-07 22:50:47,064] [INFO] Total running time: 0h1m24s