[2023-03-18 21:15:24,366] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:24,366] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:24,366] [INFO] DQC Reference Directory: /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference
[2023-03-18 21:15:25,455] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:25,455] [INFO] Task started: Prodigal
[2023-03-18 21:15:25,455] [INFO] Running command: cat /var/lib/cwl/stgab1fb0ef-2b9b-47a5-af53-bf8d46c5dc1a/OceanDNA-b30675.fa | prodigal -d OceanDNA-b30675/cds.fna -a OceanDNA-b30675/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:43,371] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:43,372] [INFO] Task started: HMMsearch
[2023-03-18 21:15:43,372] [INFO] Running command: hmmsearch --tblout OceanDNA-b30675/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/reference_markers.hmm OceanDNA-b30675/protein.faa > /dev/null
[2023-03-18 21:15:43,540] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:43,540] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab1fb0ef-2b9b-47a5-af53-bf8d46c5dc1a/OceanDNA-b30675.fa]
[2023-03-18 21:15:43,556] [INFO] Query marker FASTA was written to OceanDNA-b30675/markers.fasta
[2023-03-18 21:15:43,557] [INFO] Task started: Blastn
[2023-03-18 21:15:43,557] [INFO] Running command: blastn -query OceanDNA-b30675/markers.fasta -db /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/reference_markers.fasta -out OceanDNA-b30675/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:44,165] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:44,165] [INFO] Selected 24 target genomes.
[2023-03-18 21:15:44,166] [INFO] Target genome list was writen to OceanDNA-b30675/target_genomes.txt
[2023-03-18 21:15:44,178] [INFO] Task started: fastANI
[2023-03-18 21:15:44,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgab1fb0ef-2b9b-47a5-af53-bf8d46c5dc1a/OceanDNA-b30675.fa --refList OceanDNA-b30675/target_genomes.txt --output OceanDNA-b30675/fastani_result.tsv --threads 1
[2023-03-18 21:15:59,102] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:59,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:59,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:59,115] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:59,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:15:59,115] [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 rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.4895	270	890	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.1907	289	890	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.0421	219	890	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.0401	217	890	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.97	226	890	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.8784	197	890	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.8653	212	890	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.854	213	890	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.7504	171	890	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.6248	186	890	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.5133	191	890	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.4339	180	890	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.3214	147	890	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2265	167	890	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.2219	121	890	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.217	128	890	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.2039	144	890	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	76.1956	124	890	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.1847	135	890	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	76.1341	112	890	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	76.1002	154	890	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	76.0661	156	890	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	75.8526	135	890	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	75.8507	135	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:15:59,115] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30675/tc_result.tsv
[2023-03-18 21:15:59,115] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:59,115] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:59,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/checkm_data
[2023-03-18 21:15:59,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:59,120] [INFO] Task started: CheckM
[2023-03-18 21:15:59,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30675/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30675/checkm_input OceanDNA-b30675/checkm_result
[2023-03-18 21:16:45,215] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:45,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:45,218] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:45,218] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:45,218] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30675/markers.fasta)
[2023-03-18 21:16:45,219] [INFO] Task started: Blastn
[2023-03-18 21:16:45,219] [INFO] Running command: blastn -query OceanDNA-b30675/markers.fasta -db /var/lib/cwl/stga2bbb70b-f5ab-4e64-a489-d541e1d89753/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30675/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:46,246] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:46,247] [INFO] Selected 17 target genomes.
[2023-03-18 21:16:46,247] [INFO] Target genome list was writen to OceanDNA-b30675/target_genomes_gtdb.txt
[2023-03-18 21:16:46,259] [INFO] Task started: fastANI
[2023-03-18 21:16:46,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgab1fb0ef-2b9b-47a5-af53-bf8d46c5dc1a/OceanDNA-b30675.fa --refList OceanDNA-b30675/target_genomes_gtdb.txt --output OceanDNA-b30675/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:57,463] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:57,473] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:57,474] [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_002378665.1	s__Yoonia sp002378665	79.3448	463	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCA_905182645.1	s__Yoonia sp905182645	78.3615	317	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	77.5258	290	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	77.423	294	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCA_017854565.1	s__Yoonia sp017854565	77.3556	273	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.3045	290	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551805.1	s__Yoonia sp003551805	77.1511	198	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.0559	230	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.0278	218	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900143545.1	s__Yoonia sp900143545	76.9755	260	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199395.1	s__Yoonia ponticola	76.9589	227	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	76.89	196	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.7607	221	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.5133	191	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	76.3778	145	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	76.3348	146	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_003122215.1	s__Pararhodobacter marinus	76.1341	112	890	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:57,474] [INFO] GTDB search result was written to OceanDNA-b30675/result_gtdb.tsv
[2023-03-18 21:16:57,474] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:57,476] [INFO] DFAST_QC result json was written to OceanDNA-b30675/dqc_result.json
[2023-03-18 21:16:57,476] [INFO] DFAST_QC completed!
[2023-03-18 21:16:57,476] [INFO] Total running time: 0h1m33s