[2023-03-15 22:23:01,928] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference
[2023-03-15 22:23:03,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,675] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,675] [INFO] Running command: cat /var/lib/cwl/stg98c30199-0a62-4ec7-8727-9d0778c07414/OceanDNA-b27565.fa | prodigal -d OceanDNA-b27565/cds.fna -a OceanDNA-b27565/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:19,853] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:19,853] [INFO] Task started: HMMsearch
[2023-03-15 22:23:19,853] [INFO] Running command: hmmsearch --tblout OceanDNA-b27565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/reference_markers.hmm OceanDNA-b27565/protein.faa > /dev/null
[2023-03-15 22:23:20,047] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:20,047] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg98c30199-0a62-4ec7-8727-9d0778c07414/OceanDNA-b27565.fa]
[2023-03-15 22:23:20,068] [INFO] Query marker FASTA was written to OceanDNA-b27565/markers.fasta
[2023-03-15 22:23:20,069] [INFO] Task started: Blastn
[2023-03-15 22:23:20,069] [INFO] Running command: blastn -query OceanDNA-b27565/markers.fasta -db /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/reference_markers.fasta -out OceanDNA-b27565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:20,773] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:20,774] [INFO] Selected 28 target genomes.
[2023-03-15 22:23:20,774] [INFO] Target genome list was writen to OceanDNA-b27565/target_genomes.txt
[2023-03-15 22:23:20,816] [INFO] Task started: fastANI
[2023-03-15 22:23:20,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c30199-0a62-4ec7-8727-9d0778c07414/OceanDNA-b27565.fa --refList OceanDNA-b27565/target_genomes.txt --output OceanDNA-b27565/fastani_result.tsv --threads 1
[2023-03-15 22:23:39,908] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:39,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:39,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:39,924] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:39,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:23:39,925] [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
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	78.2752	351	829	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	78.0756	298	829	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	78.03	324	829	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.4831	289	829	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.4813	245	829	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.4526	283	829	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.4388	250	829	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.388	262	829	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.3815	240	829	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.3747	268	829	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.3705	243	829	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.3394	270	829	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.3274	303	829	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	77.3169	295	829	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.1797	252	829	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	77.1546	203	829	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.1467	209	829	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	77.0984	205	829	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.0535	228	829	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.0428	210	829	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.9775	272	829	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	76.9624	271	829	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9428	241	829	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.8137	208	829	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	76.7693	197	829	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.7149	176	829	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.4027	148	829	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2258	151	829	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:23:39,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27565/tc_result.tsv
[2023-03-15 22:23:39,925] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:39,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:39,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/checkm_data
[2023-03-15 22:23:39,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:40,033] [INFO] Task started: CheckM
[2023-03-15 22:23:40,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27565/checkm_input OceanDNA-b27565/checkm_result
[2023-03-15 22:24:22,821] [INFO] Task succeeded: CheckM
[2023-03-15 22:24:22,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:24:22,824] [INFO] ===== Completeness check finished =====
[2023-03-15 22:24:22,824] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:24:22,825] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27565/markers.fasta)
[2023-03-15 22:24:22,826] [INFO] Task started: Blastn
[2023-03-15 22:24:22,826] [INFO] Running command: blastn -query OceanDNA-b27565/markers.fasta -db /var/lib/cwl/stg47740d97-534d-4c63-8526-abc9c36f8645/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:24:24,062] [INFO] Task succeeded: Blastn
[2023-03-15 22:24:24,063] [INFO] Selected 27 target genomes.
[2023-03-15 22:24:24,063] [INFO] Target genome list was writen to OceanDNA-b27565/target_genomes_gtdb.txt
[2023-03-15 22:24:24,073] [INFO] Task started: fastANI
[2023-03-15 22:24:24,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c30199-0a62-4ec7-8727-9d0778c07414/OceanDNA-b27565.fa --refList OceanDNA-b27565/target_genomes_gtdb.txt --output OceanDNA-b27565/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:24:41,739] [INFO] Task succeeded: fastANI
[2023-03-15 22:24:41,754] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:24:41,754] [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_009993005.1	s__JAACUH01 sp009993005	78.4375	355	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_000382265.1	s__Yoonia vestfoldensis	78.2803	352	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125575.1	s__JAACUH01 sp016125575	78.1055	367	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	78.0992	342	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	78.0272	324	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	77.9508	359	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065155.1	s__SW4 sp002732825	77.6183	329	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
GCF_900108275.1	s__Jhaorihella thermophila	77.6102	252	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.6009	311	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.5994	276	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.4857	298	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	77.4813	245	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCA_017390475.1	s__Yoonia sp017390475	77.4305	294	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	77.3993	298	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.3862	265	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	77.3815	240	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016521575.1	s__Sedimentitalea sp016521575	77.3351	216	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551805.1	s__Yoonia sp003551805	77.3291	218	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCF_900184895.1	s__Flavimaricola marinus	77.3257	294	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.2951	252	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	77.2328	241	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	77.1692	232	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	77.1123	227	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.0528	229	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004751985.1	s__Rhodophyticola sp004751985	77.0317	194	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	76.6575	181	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298485.1	s__JAAFHS01 sp013298485	76.3696	149	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAFHS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:24:41,755] [INFO] GTDB search result was written to OceanDNA-b27565/result_gtdb.tsv
[2023-03-15 22:24:41,755] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:24:41,758] [INFO] DFAST_QC result json was written to OceanDNA-b27565/dqc_result.json
[2023-03-15 22:24:41,758] [INFO] DFAST_QC completed!
[2023-03-15 22:24:41,758] [INFO] Total running time: 0h1m40s