[2023-03-15 17:26:39,557] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:26:39,557] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:26:39,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference
[2023-03-15 17:26:40,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:26:40,631] [INFO] Task started: Prodigal
[2023-03-15 17:26:40,631] [INFO] Running command: cat /var/lib/cwl/stgc80242a1-308d-4954-a234-5a603c6903ef/OceanDNA-b30162.fa | prodigal -d OceanDNA-b30162/cds.fna -a OceanDNA-b30162/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:27:03,143] [INFO] Task succeeded: Prodigal
[2023-03-15 17:27:03,143] [INFO] Task started: HMMsearch
[2023-03-15 17:27:03,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b30162/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/reference_markers.hmm OceanDNA-b30162/protein.faa > /dev/null
[2023-03-15 17:27:03,339] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:27:03,340] [INFO] Found 6/6 markers.
[2023-03-15 17:27:03,363] [INFO] Query marker FASTA was written to OceanDNA-b30162/markers.fasta
[2023-03-15 17:27:03,363] [INFO] Task started: Blastn
[2023-03-15 17:27:03,364] [INFO] Running command: blastn -query OceanDNA-b30162/markers.fasta -db /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/reference_markers.fasta -out OceanDNA-b30162/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:27:04,083] [INFO] Task succeeded: Blastn
[2023-03-15 17:27:04,084] [INFO] Selected 24 target genomes.
[2023-03-15 17:27:04,085] [INFO] Target genome list was writen to OceanDNA-b30162/target_genomes.txt
[2023-03-15 17:27:04,133] [INFO] Task started: fastANI
[2023-03-15 17:27:04,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80242a1-308d-4954-a234-5a603c6903ef/OceanDNA-b30162.fa --refList OceanDNA-b30162/target_genomes.txt --output OceanDNA-b30162/fastani_result.tsv --threads 1
[2023-03-15 17:27:21,909] [INFO] Task succeeded: fastANI
[2023-03-15 17:27:21,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:27:21,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:27:21,938] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:27:21,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:27:21,939] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.7259	338	1167	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.5256	290	1167	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.4927	297	1167	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.3375	234	1167	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.1082	175	1167	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.0989	260	1167	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	77.0607	209	1167	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.9876	209	1167	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.9767	207	1167	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.949	216	1167	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.9352	227	1167	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	76.9059	165	1167	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	76.7826	172	1167	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	76.725	227	1167	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	76.7042	228	1167	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	76.6995	171	1167	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.6344	194	1167	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	76.6087	172	1167	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	76.5329	113	1167	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.47	173	1167	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	76.4031	174	1167	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.398	164	1167	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	76.3222	183	1167	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	76.1675	163	1167	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:27:21,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30162/tc_result.tsv
[2023-03-15 17:27:21,940] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:27:21,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:27:21,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/checkm_data
[2023-03-15 17:27:21,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:27:21,946] [INFO] Task started: CheckM
[2023-03-15 17:27:21,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30162/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30162/checkm_input OceanDNA-b30162/checkm_result
[2023-03-15 17:28:21,065] [INFO] Task succeeded: CheckM
[2023-03-15 17:28:21,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:28:21,074] [INFO] ===== Completeness check finished =====
[2023-03-15 17:28:21,075] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:28:21,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30162/markers.fasta)
[2023-03-15 17:28:21,076] [INFO] Task started: Blastn
[2023-03-15 17:28:21,076] [INFO] Running command: blastn -query OceanDNA-b30162/markers.fasta -db /var/lib/cwl/stgb413496e-f89a-4ec9-8fa4-2028b4cba9d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30162/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:28:22,505] [INFO] Task succeeded: Blastn
[2023-03-15 17:28:22,507] [INFO] Selected 28 target genomes.
[2023-03-15 17:28:22,507] [INFO] Target genome list was writen to OceanDNA-b30162/target_genomes_gtdb.txt
[2023-03-15 17:28:22,531] [INFO] Task started: fastANI
[2023-03-15 17:28:22,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80242a1-308d-4954-a234-5a603c6903ef/OceanDNA-b30162.fa --refList OceanDNA-b30162/target_genomes_gtdb.txt --output OceanDNA-b30162/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:28:42,538] [INFO] Task succeeded: fastANI
[2023-03-15 17:28:42,553] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:28:42,554] [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_009830125.1	s__GH1-50 sp009830125	77.7259	338	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	77.5256	290	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.3728	282	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	77.323	250	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.2906	262	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184805.1	s__Rhodobacter_B sp013184805	77.2231	225	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	77.2	263	1167	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_001482405.1	s__Ponticoccus marisrubri	77.1823	278	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	77.1523	210	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.1445	223	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	77.119	258	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	77.0998	236	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.0828	242	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCF_900142935.1	s__Rhodovulum sp900142935	77.061	217	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	76.9876	209	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014075275.1	s__Boseongicola sp014075275	76.9806	144	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCF_004342445.1	s__Rhodovulum euryhalinum	76.9764	207	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	76.8738	190	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	76.8296	201	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	76.7994	183	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	76.7395	229	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	76.7344	226	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002783145.1	s__Nioella sp002783145	76.6806	157	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.5712	180	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	76.4813	172	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	76.398	164	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_003709565.1	s__Paracoccus siganidrum	76.3322	182	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_013042895.1	s__Boseongicola sp013042895	76.3188	71	1167	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	98.28	98.28	0.61	0.61	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:28:42,555] [INFO] GTDB search result was written to OceanDNA-b30162/result_gtdb.tsv
[2023-03-15 17:28:42,556] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:28:42,560] [INFO] DFAST_QC result json was written to OceanDNA-b30162/dqc_result.json
[2023-03-15 17:28:42,560] [INFO] DFAST_QC completed!
[2023-03-15 17:28:42,560] [INFO] Total running time: 0h2m3s