[2023-03-15 11:09:10,785] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,785] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference
[2023-03-15 11:09:11,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:11,974] [INFO] Task started: Prodigal
[2023-03-15 11:09:11,975] [INFO] Running command: cat /var/lib/cwl/stgf2aadfc1-558c-4115-9eee-226b8f3298b6/OceanDNA-b27589.fa | prodigal -d OceanDNA-b27589/cds.fna -a OceanDNA-b27589/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:30,407] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:30,407] [INFO] Task started: HMMsearch
[2023-03-15 11:09:30,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b27589/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/reference_markers.hmm OceanDNA-b27589/protein.faa > /dev/null
[2023-03-15 11:09:30,658] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:30,659] [INFO] Found 6/6 markers.
[2023-03-15 11:09:30,677] [INFO] Query marker FASTA was written to OceanDNA-b27589/markers.fasta
[2023-03-15 11:09:30,677] [INFO] Task started: Blastn
[2023-03-15 11:09:30,677] [INFO] Running command: blastn -query OceanDNA-b27589/markers.fasta -db /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/reference_markers.fasta -out OceanDNA-b27589/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:31,527] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:31,528] [INFO] Selected 33 target genomes.
[2023-03-15 11:09:31,528] [INFO] Target genome list was writen to OceanDNA-b27589/target_genomes.txt
[2023-03-15 11:09:31,547] [INFO] Task started: fastANI
[2023-03-15 11:09:31,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aadfc1-558c-4115-9eee-226b8f3298b6/OceanDNA-b27589.fa --refList OceanDNA-b27589/target_genomes.txt --output OceanDNA-b27589/fastani_result.tsv --threads 1
[2023-03-15 11:09:52,677] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:52,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:52,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:52,695] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:52,695] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:52,695] [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
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.0554	217	910	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.9339	180	910	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.9013	170	910	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.8499	192	910	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.83	155	910	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	76.8244	154	910	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.7989	177	910	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	76.7862	158	910	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.7745	146	910	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7571	155	910	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.7008	191	910	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.6759	181	910	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.6758	181	910	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	76.6426	159	910	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6308	153	910	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.5944	176	910	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.5897	155	910	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.5875	156	910	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.5664	156	910	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.5319	172	910	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	76.5247	122	910	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.4884	122	910	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.4882	121	910	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	76.4765	136	910	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.4643	158	910	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.4439	157	910	95	below_threshold
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	76.4029	161	910	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	76.381	163	910	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.3745	141	910	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.3656	163	910	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	76.3071	146	910	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.2905	160	910	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	76.2281	137	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:52,695] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27589/tc_result.tsv
[2023-03-15 11:09:52,696] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:52,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:52,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/checkm_data
[2023-03-15 11:09:52,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:52,726] [INFO] Task started: CheckM
[2023-03-15 11:09:52,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27589/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27589/checkm_input OceanDNA-b27589/checkm_result
[2023-03-15 11:10:42,547] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:42,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:42,550] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:42,551] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:42,551] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27589/markers.fasta)
[2023-03-15 11:10:42,551] [INFO] Task started: Blastn
[2023-03-15 11:10:42,551] [INFO] Running command: blastn -query OceanDNA-b27589/markers.fasta -db /var/lib/cwl/stg60c9c11b-bb4b-42b0-9487-2add0542a565/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27589/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:44,027] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:44,028] [INFO] Selected 34 target genomes.
[2023-03-15 11:10:44,029] [INFO] Target genome list was writen to OceanDNA-b27589/target_genomes_gtdb.txt
[2023-03-15 11:10:44,052] [INFO] Task started: fastANI
[2023-03-15 11:10:44,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aadfc1-558c-4115-9eee-226b8f3298b6/OceanDNA-b27589.fa --refList OceanDNA-b27589/target_genomes_gtdb.txt --output OceanDNA-b27589/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:04,296] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:04,315] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:11:04,315] [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_001507595.1	s__Ruegeria marisrubri	77.107	185	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.0574	216	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_003944755.1	s__Rhodovulum robiginosum	76.8866	171	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.8499	192	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	76.83	155	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.8056	202	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.7989	177	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	76.7984	203	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	76.71	150	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	76.7068	168	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.7008	191	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.681	204	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.6758	181	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	76.6702	219	910	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_004000255.1	s__Nioella ostreopsis	76.6317	178	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747325.1	s__GCA-2747325 sp002747325	76.5686	91	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-2747325	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.5664	156	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	76.5525	124	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900537075.1	s__Ruegeria_E sp900537075	76.5493	128	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	76.5435	171	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_002073975.1	s__Rhodovulum sp002073975	76.5413	142	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172375.1	s__Aquimixticola soesokkakensis	76.5247	122	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquimixticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.4884	122	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.4594	107	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.4441	157	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_017743935.1	s__Ruegeria_E sp017743935	76.4284	154	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307765.1	s__Aliiroseovarius crassostreae	76.3693	164	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	-
GCF_900177545.1	s__Muriiphilus sp900177545	76.3587	130	910	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	76.353	177	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	76.3528	137	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746935.1	s__Muriiphilus sp002746935	76.3214	108	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048265.1	s__Paracoccus hibiscisoli	76.3071	146	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_002871005.1	s__Acidimangrovimonas sediminis	76.2939	139	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	76.2905	160	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:04,315] [INFO] GTDB search result was written to OceanDNA-b27589/result_gtdb.tsv
[2023-03-15 11:11:04,316] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:04,319] [INFO] DFAST_QC result json was written to OceanDNA-b27589/dqc_result.json
[2023-03-15 11:11:04,319] [INFO] DFAST_QC completed!
[2023-03-15 11:11:04,319] [INFO] Total running time: 0h1m54s