[2023-03-17 05:59:11,018] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,018] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference
[2023-03-17 05:59:12,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stg608048d2-830e-404b-9a50-cfc7ca478c78/OceanDNA-b27571.fa | prodigal -d OceanDNA-b27571/cds.fna -a OceanDNA-b27571/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:25,538] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:25,538] [INFO] Task started: HMMsearch
[2023-03-17 05:59:25,538] [INFO] Running command: hmmsearch --tblout OceanDNA-b27571/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/reference_markers.hmm OceanDNA-b27571/protein.faa > /dev/null
[2023-03-17 05:59:25,721] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:25,721] [INFO] Found 6/6 markers.
[2023-03-17 05:59:25,740] [INFO] Query marker FASTA was written to OceanDNA-b27571/markers.fasta
[2023-03-17 05:59:25,740] [INFO] Task started: Blastn
[2023-03-17 05:59:25,741] [INFO] Running command: blastn -query OceanDNA-b27571/markers.fasta -db /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/reference_markers.fasta -out OceanDNA-b27571/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:26,467] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:26,468] [INFO] Selected 38 target genomes.
[2023-03-17 05:59:26,468] [INFO] Target genome list was writen to OceanDNA-b27571/target_genomes.txt
[2023-03-17 05:59:26,484] [INFO] Task started: fastANI
[2023-03-17 05:59:26,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg608048d2-830e-404b-9a50-cfc7ca478c78/OceanDNA-b27571.fa --refList OceanDNA-b27571/target_genomes.txt --output OceanDNA-b27571/fastani_result.tsv --threads 1
[2023-03-17 05:59:50,348] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:50,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:50,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:50,366] [INFO] Found 37 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:50,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:50,367] [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
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.5802	136	708	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.5786	136	708	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	77.5039	133	708	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	77.4119	137	708	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.3206	135	708	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.317	147	708	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.241	147	708	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	77.1786	112	708	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.1108	117	708	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	77.0645	101	708	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.9934	122	708	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.9083	120	708	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.8143	122	708	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.7836	111	708	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.7836	111	708	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.7781	120	708	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.7464	120	708	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.735	89	708	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.7147	112	708	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	76.6537	79	708	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	76.6189	88	708	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6051	87	708	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.5513	85	708	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.5472	66	708	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.5395	66	708	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.4353	111	708	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.4279	80	708	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.4186	97	708	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.2094	77	708	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.2073	60	708	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.0624	69	708	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.04	61	708	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	75.9843	75	708	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	75.9843	75	708	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.9655	65	708	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.9048	64	708	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	75.6753	62	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:50,367] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27571/tc_result.tsv
[2023-03-17 05:59:50,367] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:50,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:50,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/checkm_data
[2023-03-17 05:59:50,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:50,503] [INFO] Task started: CheckM
[2023-03-17 05:59:50,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27571/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27571/checkm_input OceanDNA-b27571/checkm_result
[2023-03-17 06:00:27,617] [INFO] Task succeeded: CheckM
[2023-03-17 06:00:27,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.81%
Contamintation: 3.94%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 06:00:27,620] [INFO] ===== Completeness check finished =====
[2023-03-17 06:00:27,620] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:00:27,620] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27571/markers.fasta)
[2023-03-17 06:00:27,620] [INFO] Task started: Blastn
[2023-03-17 06:00:27,620] [INFO] Running command: blastn -query OceanDNA-b27571/markers.fasta -db /var/lib/cwl/stg42ebbd51-c4c5-41b8-918f-23fd7c45af6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27571/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:00:28,907] [INFO] Task succeeded: Blastn
[2023-03-17 06:00:28,908] [INFO] Selected 37 target genomes.
[2023-03-17 06:00:28,908] [INFO] Target genome list was writen to OceanDNA-b27571/target_genomes_gtdb.txt
[2023-03-17 06:00:29,148] [INFO] Task started: fastANI
[2023-03-17 06:00:29,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg608048d2-830e-404b-9a50-cfc7ca478c78/OceanDNA-b27571.fa --refList OceanDNA-b27571/target_genomes_gtdb.txt --output OceanDNA-b27571/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:00:57,560] [INFO] Task succeeded: fastANI
[2023-03-17 06:00:57,579] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:00:57,579] [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_002285415.1	s__Actibacterium pelagium	77.5802	136	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	77.5277	132	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003355.1	s__Donghicola tyrosinivorans	77.4119	137	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	77.3203	146	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_004799325.1	s__Thalassobius vesicularis	77.2884	151	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	77.2738	127	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_009857745.1	s__Thalassobius mangrovi	77.2187	154	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	77.2101	107	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115865.1	s__Donghicola eburneus	77.1816	111	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	99.41	99.41	0.91	0.91	2	-
GCF_016888515.1	s__Shimia_A biformata	77.1522	153	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	77.1273	127	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	77.1098	141	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_900327775.1	s__Roseovarius sp900327775	77.0666	76	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872875.1	s__WKFI01 sp014872875	77.0568	122	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.0083	128	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	76.9929	126	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	76.837	117	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.8143	122	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	76.8085	123	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_013317235.1	s__Leisingera sp013317235	76.7916	122	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	76.7836	111	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009669325.1	s__Roseovarius bejariae	76.7464	120	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001730095.1	s__Leisingera sp001730095	76.7236	117	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	76.7135	111	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	76.6793	105	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_010500245.1	s__Ruegeria_B sp010500245	76.642	143	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	76.5987	118	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	76.5513	85	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.5348	65	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009924775.1	s__Lutimaribacter sp009924775	76.4449	70	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.4227	79	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.3863	114	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_000223375.1	s__Ketogulonicigenium vulgare	76.2359	51	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ketogulonicigenium	95.0	99.98	99.96	1.00	1.00	5	-
GCF_900156535.1	s__Roseovarius nanhaiticus	76.1499	73	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003058085.1	s__Yoonia sediminilitoris	75.9727	74	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 06:00:57,579] [INFO] GTDB search result was written to OceanDNA-b27571/result_gtdb.tsv
[2023-03-17 06:00:57,579] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:00:57,583] [INFO] DFAST_QC result json was written to OceanDNA-b27571/dqc_result.json
[2023-03-17 06:00:57,583] [INFO] DFAST_QC completed!
[2023-03-17 06:00:57,583] [INFO] Total running time: 0h1m47s