[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference
[2023-03-19 01:50:03,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,566] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,566] [INFO] Running command: cat /var/lib/cwl/stg7b40f1e7-7797-4c59-9a00-43274013e873/OceanDNA-b30535.fa | prodigal -d OceanDNA-b30535/cds.fna -a OceanDNA-b30535/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:24,024] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:24,024] [INFO] Task started: HMMsearch
[2023-03-19 01:50:24,024] [INFO] Running command: hmmsearch --tblout OceanDNA-b30535/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/reference_markers.hmm OceanDNA-b30535/protein.faa > /dev/null
[2023-03-19 01:50:24,229] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:24,229] [INFO] Found 6/6 markers.
[2023-03-19 01:50:24,252] [INFO] Query marker FASTA was written to OceanDNA-b30535/markers.fasta
[2023-03-19 01:50:24,254] [INFO] Task started: Blastn
[2023-03-19 01:50:24,254] [INFO] Running command: blastn -query OceanDNA-b30535/markers.fasta -db /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/reference_markers.fasta -out OceanDNA-b30535/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:24,933] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:24,934] [INFO] Selected 25 target genomes.
[2023-03-19 01:50:24,934] [INFO] Target genome list was writen to OceanDNA-b30535/target_genomes.txt
[2023-03-19 01:50:24,954] [INFO] Task started: fastANI
[2023-03-19 01:50:24,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b40f1e7-7797-4c59-9a00-43274013e873/OceanDNA-b30535.fa --refList OceanDNA-b30535/target_genomes.txt --output OceanDNA-b30535/fastani_result.tsv --threads 1
[2023-03-19 01:50:40,612] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:40,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:40,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:40,626] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:40,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:40,626] [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
Thalassobacter stenotrophicus	strain=DSM 16310	GCA_900141945.1	266809	266809	type	True	88.0936	867	1043	95	below_threshold
Thalassobacter stenotrophicus	strain=CECT 5294	GCA_001458315.1	266809	266809	type	True	88.0387	878	1043	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.1906	162	1043	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	77.1716	118	1043	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.0805	133	1043	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.9282	68	1043	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.787	113	1043	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	76.7753	122	1043	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.6335	133	1043	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.6222	125	1043	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.5504	120	1043	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.495	111	1043	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.4526	101	1043	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	76.4209	95	1043	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.3836	108	1043	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.3156	90	1043	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.3156	90	1043	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	76.2727	106	1043	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.2434	85	1043	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.1597	102	1043	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.1001	112	1043	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.0392	72	1043	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	75.9982	66	1043	95	below_threshold
Paracoccus aminophilus	strain=JCM 7686	GCA_000444995.1	34003	34003	type	True	75.9569	79	1043	95	below_threshold
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	75.8935	67	1043	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:40,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30535/tc_result.tsv
[2023-03-19 01:50:40,627] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:40,627] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:40,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/checkm_data
[2023-03-19 01:50:40,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:40,666] [INFO] Task started: CheckM
[2023-03-19 01:50:40,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30535/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30535/checkm_input OceanDNA-b30535/checkm_result
[2023-03-19 01:51:33,004] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:33,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.45%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:33,019] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:33,020] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:33,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30535/markers.fasta)
[2023-03-19 01:51:33,021] [INFO] Task started: Blastn
[2023-03-19 01:51:33,021] [INFO] Running command: blastn -query OceanDNA-b30535/markers.fasta -db /var/lib/cwl/stgc315ade7-2a47-4306-8ae0-4853885b7fbc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30535/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:34,210] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:34,211] [INFO] Selected 28 target genomes.
[2023-03-19 01:51:34,212] [INFO] Target genome list was writen to OceanDNA-b30535/target_genomes_gtdb.txt
[2023-03-19 01:51:34,237] [INFO] Task started: fastANI
[2023-03-19 01:51:34,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b40f1e7-7797-4c59-9a00-43274013e873/OceanDNA-b30535.fa --refList OceanDNA-b30535/target_genomes_gtdb.txt --output OceanDNA-b30535/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:51,701] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:51,716] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:51:51,716] [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_001458315.1	s__Thalassobacter stenotrophicus	88.0387	878	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobacter	95.0	98.03	96.21	0.91	0.88	5	-
GCA_017643305.1	s__HXMU1420-2 sp017643305	77.3354	103	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HXMU1420-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364805.1	s__Pelagimonas phthalicica	77.1597	117	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCA_006844665.1	s__Dinoroseobacter sp006844665	77.0231	90	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346865.1	s__Shimia isoporae	76.9662	67	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	76.9453	117	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.7711	112	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	76.75	127	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031585.1	s__Halocynthiibacter sp003031585	76.7393	77	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	76.7318	121	1043	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_003335585.1	s__Sulfitobacter sp003335585	76.7212	137	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	76.6958	102	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.6811	124	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	76.6005	130	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCA_018402175.1	s__Yoonia sp018402175	76.5221	111	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_900172335.1	s__Roseovarius albus	76.5198	93	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	76.4455	111	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_013032455.1	s__Ruegeria atlantica_B	76.435	111	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.37	96.74	0.95	0.90	3	-
GCF_015644665.1	s__Roseobacter sp015644665	76.4289	128	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.3999	131	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001879695.1	s__Nioella sediminis	76.3692	106	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003058085.1	s__Yoonia sediminilitoris	76.3556	111	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792405.1	s__Vannielia sp017792405	76.3533	107	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.2785	134	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	76.2675	103	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080415.1	s__Roseovarius mucosus_A	76.2248	116	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.2201	109	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.1144	111	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:51,717] [INFO] GTDB search result was written to OceanDNA-b30535/result_gtdb.tsv
[2023-03-19 01:51:51,717] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:51,725] [INFO] DFAST_QC result json was written to OceanDNA-b30535/dqc_result.json
[2023-03-19 01:51:51,725] [INFO] DFAST_QC completed!
[2023-03-19 01:51:51,725] [INFO] Total running time: 0h1m50s