[2023-03-15 05:29:12,472] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,472] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference
[2023-03-15 05:29:13,556] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,556] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,556] [INFO] Running command: cat /var/lib/cwl/stg6a1a080d-01f7-41b9-9d7e-bc74295be8e7/OceanDNA-b27536.fa | prodigal -d OceanDNA-b27536/cds.fna -a OceanDNA-b27536/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:31,324] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:31,324] [INFO] Task started: HMMsearch
[2023-03-15 05:29:31,324] [INFO] Running command: hmmsearch --tblout OceanDNA-b27536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/reference_markers.hmm OceanDNA-b27536/protein.faa > /dev/null
[2023-03-15 05:29:31,550] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:31,551] [INFO] Found 6/6 markers.
[2023-03-15 05:29:31,569] [INFO] Query marker FASTA was written to OceanDNA-b27536/markers.fasta
[2023-03-15 05:29:31,569] [INFO] Task started: Blastn
[2023-03-15 05:29:31,569] [INFO] Running command: blastn -query OceanDNA-b27536/markers.fasta -db /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/reference_markers.fasta -out OceanDNA-b27536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:32,179] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:32,180] [INFO] Selected 35 target genomes.
[2023-03-15 05:29:32,180] [INFO] Target genome list was writen to OceanDNA-b27536/target_genomes.txt
[2023-03-15 05:29:32,197] [INFO] Task started: fastANI
[2023-03-15 05:29:32,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a1a080d-01f7-41b9-9d7e-bc74295be8e7/OceanDNA-b27536.fa --refList OceanDNA-b27536/target_genomes.txt --output OceanDNA-b27536/fastani_result.tsv --threads 1
[2023-03-15 05:29:53,993] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:53,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:53,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:54,010] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:54,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:54,010] [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
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	76.478	108	883	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.4592	102	883	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.3634	77	883	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	76.3619	93	883	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.333	133	883	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	76.3047	134	883	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	76.3017	94	883	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	76.3001	75	883	95	below_threshold
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	76.2815	94	883	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	76.2782	92	883	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	76.2768	90	883	95	below_threshold
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	76.2751	95	883	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	76.2645	131	883	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.2589	76	883	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	76.2568	76	883	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.2153	78	883	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	76.2094	66	883	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	76.1826	68	883	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.1735	101	883	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	76.1671	103	883	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.1343	125	883	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.1323	62	883	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.1298	90	883	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	76.0822	70	883	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.053	67	883	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	75.9791	63	883	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	75.9449	62	883	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	75.9194	59	883	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	75.9088	78	883	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	75.8891	74	883	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	75.8813	60	883	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	75.8731	67	883	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	75.8198	67	883	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:54,010] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27536/tc_result.tsv
[2023-03-15 05:29:54,011] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:54,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:54,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/checkm_data
[2023-03-15 05:29:54,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:54,016] [INFO] Task started: CheckM
[2023-03-15 05:29:54,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27536/checkm_input OceanDNA-b27536/checkm_result
[2023-03-15 05:30:41,438] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:41,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:41,451] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:41,451] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:41,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27536/markers.fasta)
[2023-03-15 05:30:41,453] [INFO] Task started: Blastn
[2023-03-15 05:30:41,453] [INFO] Running command: blastn -query OceanDNA-b27536/markers.fasta -db /var/lib/cwl/stg91e03db2-c3c5-43df-abbe-7a2c3e4f02e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:42,329] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:42,330] [INFO] Selected 35 target genomes.
[2023-03-15 05:30:42,330] [INFO] Target genome list was writen to OceanDNA-b27536/target_genomes_gtdb.txt
[2023-03-15 05:30:42,366] [INFO] Task started: fastANI
[2023-03-15 05:30:42,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a1a080d-01f7-41b9-9d7e-bc74295be8e7/OceanDNA-b27536.fa --refList OceanDNA-b27536/target_genomes_gtdb.txt --output OceanDNA-b27536/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:31:02,242] [INFO] Task succeeded: fastANI
[2023-03-15 05:31:02,259] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:31:02,259] [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_004015795.1	s__Falsirhodobacter deserti	76.8229	51	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	76.6772	105	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	76.5958	101	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	76.478	108	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422085.1	s__Phaeovulum sp002422085	76.4769	99	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155295.1	s__Pseudogemmobacter sp013155295	76.3884	76	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	76.3732	92	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	76.3295	132	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_009908165.1	s__Frigidibacter albus	76.2782	92	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	76.2628	125	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	76.2589	76	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	76.211	125	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCF_003352045.1	s__JL08 sp003352045	76.2064	88	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	76.1972	118	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	76.1755	55	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCA_016124615.1	s__Solirhodobacter sp016124615	76.1593	93	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	76.1498	114	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	76.1413	59	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	76.1334	128	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	76.1298	90	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	76.1158	95	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111675.1	s__Paracoccus homiensis	76.0822	70	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	75.9665	58	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286075.1	s__Paracoccus endophyticus	75.9194	59	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653255.1	s__Rhodobaculum claviforme	75.9092	55	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	75.9088	78	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057885.1	s__Oceaniglobus ichthyenteri	75.8998	97	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	75.8891	74	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	75.846	90	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	75.8309	62	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_002708925.1	s__Thalassobius sp002708925	75.7991	60	883	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:31:02,259] [INFO] GTDB search result was written to OceanDNA-b27536/result_gtdb.tsv
[2023-03-15 05:31:02,259] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:31:02,262] [INFO] DFAST_QC result json was written to OceanDNA-b27536/dqc_result.json
[2023-03-15 05:31:02,262] [INFO] DFAST_QC completed!
[2023-03-15 05:31:02,263] [INFO] Total running time: 0h1m50s