[2023-03-15 21:48:07,261] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,261] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference
[2023-03-15 21:48:08,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,886] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,886] [INFO] Running command: cat /var/lib/cwl/stgbd27d4a5-9040-41ca-bb94-8c791d45c173/OceanDNA-b27525.fa | prodigal -d OceanDNA-b27525/cds.fna -a OceanDNA-b27525/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:32,754] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:32,754] [INFO] Task started: HMMsearch
[2023-03-15 21:48:32,754] [INFO] Running command: hmmsearch --tblout OceanDNA-b27525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/reference_markers.hmm OceanDNA-b27525/protein.faa > /dev/null
[2023-03-15 21:48:32,965] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:32,966] [INFO] Found 6/6 markers.
[2023-03-15 21:48:32,991] [INFO] Query marker FASTA was written to OceanDNA-b27525/markers.fasta
[2023-03-15 21:48:32,992] [INFO] Task started: Blastn
[2023-03-15 21:48:32,993] [INFO] Running command: blastn -query OceanDNA-b27525/markers.fasta -db /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/reference_markers.fasta -out OceanDNA-b27525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:33,701] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:33,701] [INFO] Selected 30 target genomes.
[2023-03-15 21:48:33,702] [INFO] Target genome list was writen to OceanDNA-b27525/target_genomes.txt
[2023-03-15 21:48:33,747] [INFO] Task started: fastANI
[2023-03-15 21:48:33,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd27d4a5-9040-41ca-bb94-8c791d45c173/OceanDNA-b27525.fa --refList OceanDNA-b27525/target_genomes.txt --output OceanDNA-b27525/fastani_result.tsv --threads 1
[2023-03-15 21:48:51,721] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:51,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:51,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:51,737] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:51,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:51,738] [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
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.4877	172	1226	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.3985	156	1226	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.3833	160	1226	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.3674	157	1226	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.3278	143	1226	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.2901	158	1226	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.2811	150	1226	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.2792	165	1226	95	below_threshold
Coraliihabitans acroporae	strain=NNCM2	GCA_019891535.1	2834412	2834412	type	True	76.2772	122	1226	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.2726	150	1226	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.2457	136	1226	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.1916	174	1226	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.1778	137	1226	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	76.1521	120	1226	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.152	136	1226	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.1474	141	1226	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.0965	174	1226	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	76.0925	141	1226	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.0766	95	1226	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.0687	152	1226	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.0655	132	1226	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.0457	120	1226	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.0362	101	1226	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.0313	125	1226	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.9498	144	1226	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.8792	135	1226	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	75.8379	91	1226	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.7692	149	1226	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	75.7269	107	1226	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	75.6667	109	1226	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:51,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27525/tc_result.tsv
[2023-03-15 21:48:51,738] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:51,738] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:51,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/checkm_data
[2023-03-15 21:48:51,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:51,744] [INFO] Task started: CheckM
[2023-03-15 21:48:51,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27525/checkm_input OceanDNA-b27525/checkm_result
[2023-03-15 21:49:55,569] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:55,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:55,572] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:55,572] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:55,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27525/markers.fasta)
[2023-03-15 21:49:55,573] [INFO] Task started: Blastn
[2023-03-15 21:49:55,573] [INFO] Running command: blastn -query OceanDNA-b27525/markers.fasta -db /var/lib/cwl/stg02f17aef-d89c-40c6-9ae4-18c2b8b17ae1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:56,816] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:56,817] [INFO] Selected 33 target genomes.
[2023-03-15 21:49:56,817] [INFO] Target genome list was writen to OceanDNA-b27525/target_genomes_gtdb.txt
[2023-03-15 21:49:56,928] [INFO] Task started: fastANI
[2023-03-15 21:49:56,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd27d4a5-9040-41ca-bb94-8c791d45c173/OceanDNA-b27525.fa --refList OceanDNA-b27525/target_genomes_gtdb.txt --output OceanDNA-b27525/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:17,170] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:17,188] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:50:17,189] [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
GCF_002285435.1	s__Actibacterium ureilyticum	76.7207	195	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	76.5701	149	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003500165.1	s__UBA10424 sp003500165	76.5597	118	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA10424	95.0	99.72	99.62	0.98	0.98	3	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	76.5048	176	1226	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_009833495.1	s__Oceanomicrobium pacificus	76.4758	173	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.4074	168	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.3833	160	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_004339675.1	s__Rhodovulum steppense	76.3118	162	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	76.2997	157	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	76.2865	169	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	76.2457	136	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.2316	170	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313005.1	s__Roseovarius sp900313005	76.2245	101	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768555.3	s__Roseovarius mucosus	76.2028	157	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.1598	140	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900177545.1	s__Muriiphilus sp900177545	76.1339	126	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	76.1265	178	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	76.1093	89	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129775.1	s__Rhodobaculum sp007129775	76.1059	102	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	76.1019	129	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487165.1	s__UBA5972 sp015487165	76.0706	132	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	76.058	153	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	76.0546	122	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	75.9175	125	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	75.8983	139	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	75.8756	118	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCA_013151335.1	s__UBA5972 sp013151335	75.8513	99	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458195.1	s__Ruegeria atlantica	75.8379	91	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCF_000813745.1	s__Leisingera sp000813745	75.8237	132	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	75.7864	118	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	75.7689	149	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008711135.1	s__LNNU-3342 sp008711135	75.6761	98	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	75.4426	84	1226	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:17,189] [INFO] GTDB search result was written to OceanDNA-b27525/result_gtdb.tsv
[2023-03-15 21:50:17,189] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:17,192] [INFO] DFAST_QC result json was written to OceanDNA-b27525/dqc_result.json
[2023-03-15 21:50:17,192] [INFO] DFAST_QC completed!
[2023-03-15 21:50:17,192] [INFO] Total running time: 0h2m10s