[2023-03-18 00:02:09,226] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:02:09,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:02:09,226] [INFO] DQC Reference Directory: /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference
[2023-03-18 00:02:10,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:02:10,347] [INFO] Task started: Prodigal
[2023-03-18 00:02:10,347] [INFO] Running command: cat /var/lib/cwl/stgf2b5c406-b58e-44c9-ad3a-a86a3d3fa8e4/OceanDNA-b30051.fa | prodigal -d OceanDNA-b30051/cds.fna -a OceanDNA-b30051/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:02:28,214] [INFO] Task succeeded: Prodigal
[2023-03-18 00:02:28,215] [INFO] Task started: HMMsearch
[2023-03-18 00:02:28,215] [INFO] Running command: hmmsearch --tblout OceanDNA-b30051/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/reference_markers.hmm OceanDNA-b30051/protein.faa > /dev/null
[2023-03-18 00:02:28,398] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:02:28,399] [INFO] Found 6/6 markers.
[2023-03-18 00:02:28,418] [INFO] Query marker FASTA was written to OceanDNA-b30051/markers.fasta
[2023-03-18 00:02:28,419] [INFO] Task started: Blastn
[2023-03-18 00:02:28,419] [INFO] Running command: blastn -query OceanDNA-b30051/markers.fasta -db /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/reference_markers.fasta -out OceanDNA-b30051/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:29,235] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:29,236] [INFO] Selected 23 target genomes.
[2023-03-18 00:02:29,236] [INFO] Target genome list was writen to OceanDNA-b30051/target_genomes.txt
[2023-03-18 00:02:29,250] [INFO] Task started: fastANI
[2023-03-18 00:02:29,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2b5c406-b58e-44c9-ad3a-a86a3d3fa8e4/OceanDNA-b30051.fa --refList OceanDNA-b30051/target_genomes.txt --output OceanDNA-b30051/fastani_result.tsv --threads 1
[2023-03-18 00:02:44,287] [INFO] Task succeeded: fastANI
[2023-03-18 00:02:44,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:02:44,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:02:44,301] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:02:44,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:02:44,301] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.9003	450	898	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.9402	332	898	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.9115	306	898	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.898	324	898	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.8145	277	898	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.7963	318	898	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.7859	306	898	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.6603	338	898	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.5783	280	898	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.5732	291	898	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.5524	253	898	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	77.5369	256	898	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	77.4752	330	898	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4431	271	898	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	77.2128	249	898	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.1982	202	898	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	77.1965	249	898	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.1637	249	898	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.113	220	898	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.0786	222	898	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	76.9623	211	898	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	76.9407	258	898	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	76.9384	215	898	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:02:44,301] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30051/tc_result.tsv
[2023-03-18 00:02:44,301] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:02:44,301] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:02:44,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/checkm_data
[2023-03-18 00:02:44,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:02:44,307] [INFO] Task started: CheckM
[2023-03-18 00:02:44,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30051/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30051/checkm_input OceanDNA-b30051/checkm_result
[2023-03-18 00:03:36,301] [INFO] Task succeeded: CheckM
[2023-03-18 00:03:36,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:03:36,304] [INFO] ===== Completeness check finished =====
[2023-03-18 00:03:36,304] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:03:36,304] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30051/markers.fasta)
[2023-03-18 00:03:36,305] [INFO] Task started: Blastn
[2023-03-18 00:03:36,305] [INFO] Running command: blastn -query OceanDNA-b30051/markers.fasta -db /var/lib/cwl/stga2fccea6-4580-40b5-865b-b43f77eac799/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30051/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:03:38,005] [INFO] Task succeeded: Blastn
[2023-03-18 00:03:38,006] [INFO] Selected 13 target genomes.
[2023-03-18 00:03:38,006] [INFO] Target genome list was writen to OceanDNA-b30051/target_genomes_gtdb.txt
[2023-03-18 00:03:38,052] [INFO] Task started: fastANI
[2023-03-18 00:03:38,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2b5c406-b58e-44c9-ad3a-a86a3d3fa8e4/OceanDNA-b30051.fa --refList OceanDNA-b30051/target_genomes_gtdb.txt --output OceanDNA-b30051/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:03:47,131] [INFO] Task succeeded: fastANI
[2023-03-18 00:03:47,139] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:03:47,139] [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_018402035.1	s__Roseicyclus sp018402035	82.6238	639	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689735.1	s__Roseicyclus sp015689735	81.827	627	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	81.4364	498	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	80.8525	625	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401055.1	s__Roseicyclus sp018401055	80.6854	489	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.9591	579	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.7375	511	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	78.9003	450	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	77.9568	365	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCA_003428585.1	s__Nioella sp003428585	77.8192	323	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.7906	298	898	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_016938875.1	s__Rhodovulum sp016938875	77.728	314	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.715	311	898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-18 00:03:47,139] [INFO] GTDB search result was written to OceanDNA-b30051/result_gtdb.tsv
[2023-03-18 00:03:47,140] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:03:47,141] [INFO] DFAST_QC result json was written to OceanDNA-b30051/dqc_result.json
[2023-03-18 00:03:47,142] [INFO] DFAST_QC completed!
[2023-03-18 00:03:47,142] [INFO] Total running time: 0h1m38s