[2023-03-16 07:10:57,552] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:10:57,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:10:57,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference
[2023-03-16 07:10:58,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:10:58,620] [INFO] Task started: Prodigal
[2023-03-16 07:10:58,620] [INFO] Running command: cat /var/lib/cwl/stg3f53eb48-8945-4db5-a317-03db93a21e13/OceanDNA-b30667.fa | prodigal -d OceanDNA-b30667/cds.fna -a OceanDNA-b30667/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:11:12,102] [INFO] Task succeeded: Prodigal
[2023-03-16 07:11:12,103] [INFO] Task started: HMMsearch
[2023-03-16 07:11:12,103] [INFO] Running command: hmmsearch --tblout OceanDNA-b30667/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/reference_markers.hmm OceanDNA-b30667/protein.faa > /dev/null
[2023-03-16 07:11:12,283] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:11:12,284] [INFO] Found 6/6 markers.
[2023-03-16 07:11:12,303] [INFO] Query marker FASTA was written to OceanDNA-b30667/markers.fasta
[2023-03-16 07:11:12,304] [INFO] Task started: Blastn
[2023-03-16 07:11:12,304] [INFO] Running command: blastn -query OceanDNA-b30667/markers.fasta -db /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/reference_markers.fasta -out OceanDNA-b30667/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:11:13,076] [INFO] Task succeeded: Blastn
[2023-03-16 07:11:13,077] [INFO] Selected 36 target genomes.
[2023-03-16 07:11:13,078] [INFO] Target genome list was writen to OceanDNA-b30667/target_genomes.txt
[2023-03-16 07:11:13,124] [INFO] Task started: fastANI
[2023-03-16 07:11:13,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f53eb48-8945-4db5-a317-03db93a21e13/OceanDNA-b30667.fa --refList OceanDNA-b30667/target_genomes.txt --output OceanDNA-b30667/fastani_result.tsv --threads 1
[2023-03-16 07:11:34,587] [INFO] Task succeeded: fastANI
[2023-03-16 07:11:34,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:11:34,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:11:34,606] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:11:34,606] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:11:34,607] [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 tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.5087	181	667	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.0766	161	667	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.0754	173	667	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.0426	142	667	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.8782	123	667	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.8564	124	667	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	76.8128	95	667	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.6901	153	667	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.6883	106	667	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.6761	136	667	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.6749	136	667	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.6519	96	667	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.5943	110	667	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.5912	97	667	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	76.4295	68	667	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.4172	74	667	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.4079	97	667	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.3978	119	667	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.329	113	667	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.2676	87	667	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	76.2661	86	667	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	76.246	87	667	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.1655	92	667	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.137	78	667	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.1245	100	667	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.0949	77	667	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.0832	99	667	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	75.9971	75	667	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	75.8977	103	667	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	75.8488	52	667	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.8383	62	667	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.7769	58	667	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.7373	92	667	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	75.6845	77	667	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.6498	62	667	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.6498	62	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:11:34,608] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30667/tc_result.tsv
[2023-03-16 07:11:34,608] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:11:34,608] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:11:34,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/checkm_data
[2023-03-16 07:11:34,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:11:34,633] [INFO] Task started: CheckM
[2023-03-16 07:11:34,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30667/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30667/checkm_input OceanDNA-b30667/checkm_result
[2023-03-16 07:12:11,789] [INFO] Task succeeded: CheckM
[2023-03-16 07:12:11,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:12:11,794] [INFO] ===== Completeness check finished =====
[2023-03-16 07:12:11,794] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:12:11,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30667/markers.fasta)
[2023-03-16 07:12:11,796] [INFO] Task started: Blastn
[2023-03-16 07:12:11,796] [INFO] Running command: blastn -query OceanDNA-b30667/markers.fasta -db /var/lib/cwl/stg504c114e-d4fe-43c0-b0bc-b008ae1a6b1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30667/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:12:13,261] [INFO] Task succeeded: Blastn
[2023-03-16 07:12:13,262] [INFO] Selected 28 target genomes.
[2023-03-16 07:12:13,262] [INFO] Target genome list was writen to OceanDNA-b30667/target_genomes_gtdb.txt
[2023-03-16 07:12:13,442] [INFO] Task started: fastANI
[2023-03-16 07:12:13,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f53eb48-8945-4db5-a317-03db93a21e13/OceanDNA-b30667.fa --refList OceanDNA-b30667/target_genomes_gtdb.txt --output OceanDNA-b30667/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:12:29,223] [INFO] Task succeeded: fastANI
[2023-03-16 07:12:29,237] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:12:29,238] [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	79.1097	299	667	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	78.3001	204	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.4916	182	667	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	77.4448	165	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	77.3975	182	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	77.0766	161	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.0609	174	667	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	77.0426	142	667	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	76.9196	164	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	76.8954	182	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933395.1	s__Yoonia maritima_A	76.8535	95	667	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	76.8479	193	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.7463	167	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	76.6901	153	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_900110065.1	s__Loktanella fryxellensis	76.6883	106	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	76.6199	141	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110705.1	s__Loktanella sp900110705	76.5914	127	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	76.5013	134	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	76.3978	119	667	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	76.3606	84	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	76.2676	87	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_002115805.1	s__Marivita geojedonensis	76.2661	86	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004343075.1	s__Rhodovulum marinum	76.2624	70	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	76.2589	90	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900102535.1	s__Sulfitobacter delicatus	76.1655	92	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.1649	73	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	75.9694	60	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_900114635.1	s__Shimia aestuarii	75.9443	74	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:12:29,238] [INFO] GTDB search result was written to OceanDNA-b30667/result_gtdb.tsv
[2023-03-16 07:12:29,238] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:12:29,241] [INFO] DFAST_QC result json was written to OceanDNA-b30667/dqc_result.json
[2023-03-16 07:12:29,242] [INFO] DFAST_QC completed!
[2023-03-16 07:12:29,242] [INFO] Total running time: 0h1m32s