[2023-03-18 09:15:00,471] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference
[2023-03-18 09:15:02,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,044] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,044] [INFO] Running command: cat /var/lib/cwl/stg2499d822-54de-43f9-b44d-02946af278ae/OceanDNA-b27523.fa | prodigal -d OceanDNA-b27523/cds.fna -a OceanDNA-b27523/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:16,859] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:16,859] [INFO] Task started: HMMsearch
[2023-03-18 09:15:16,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b27523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/reference_markers.hmm OceanDNA-b27523/protein.faa > /dev/null
[2023-03-18 09:15:17,049] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:17,049] [INFO] Found 6/6 markers.
[2023-03-18 09:15:17,088] [INFO] Query marker FASTA was written to OceanDNA-b27523/markers.fasta
[2023-03-18 09:15:17,089] [INFO] Task started: Blastn
[2023-03-18 09:15:17,089] [INFO] Running command: blastn -query OceanDNA-b27523/markers.fasta -db /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/reference_markers.fasta -out OceanDNA-b27523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:17,779] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:17,786] [INFO] Selected 33 target genomes.
[2023-03-18 09:15:17,786] [INFO] Target genome list was writen to OceanDNA-b27523/target_genomes.txt
[2023-03-18 09:15:17,803] [INFO] Task started: fastANI
[2023-03-18 09:15:17,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg2499d822-54de-43f9-b44d-02946af278ae/OceanDNA-b27523.fa --refList OceanDNA-b27523/target_genomes.txt --output OceanDNA-b27523/fastani_result.tsv --threads 1
[2023-03-18 09:15:37,869] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:37,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:37,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:37,888] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:37,888] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:15:37,888] [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
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.4125	124	801	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.3799	117	801	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.3166	127	801	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.2351	130	801	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.1265	80	801	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.1059	123	801	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	77.0056	106	801	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.9909	81	801	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.9156	99	801	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.7558	134	801	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.6648	84	801	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.6122	124	801	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	76.5931	106	801	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.5847	110	801	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	76.5353	80	801	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	76.5296	110	801	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.484	84	801	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	76.4797	124	801	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.474	88	801	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	76.4672	109	801	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.4672	109	801	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.4053	95	801	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.3343	79	801	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.2872	89	801	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.2324	89	801	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.23	93	801	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.2146	94	801	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.1917	86	801	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.1913	86	801	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.1363	96	801	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.0747	54	801	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.9958	79	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:15:37,888] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27523/tc_result.tsv
[2023-03-18 09:15:37,888] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:37,888] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:37,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/checkm_data
[2023-03-18 09:15:37,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:37,895] [INFO] Task started: CheckM
[2023-03-18 09:15:37,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27523/checkm_input OceanDNA-b27523/checkm_result
[2023-03-18 09:16:17,954] [INFO] Task succeeded: CheckM
[2023-03-18 09:16:17,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 5.30%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:16:17,957] [INFO] ===== Completeness check finished =====
[2023-03-18 09:16:17,957] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:16:17,958] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27523/markers.fasta)
[2023-03-18 09:16:17,959] [INFO] Task started: Blastn
[2023-03-18 09:16:17,959] [INFO] Running command: blastn -query OceanDNA-b27523/markers.fasta -db /var/lib/cwl/stgc56e5c2e-2dd5-43bb-99f9-29c1655007d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:16:19,079] [INFO] Task succeeded: Blastn
[2023-03-18 09:16:19,080] [INFO] Selected 34 target genomes.
[2023-03-18 09:16:19,080] [INFO] Target genome list was writen to OceanDNA-b27523/target_genomes_gtdb.txt
[2023-03-18 09:16:19,110] [INFO] Task started: fastANI
[2023-03-18 09:16:19,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg2499d822-54de-43f9-b44d-02946af278ae/OceanDNA-b27523.fa --refList OceanDNA-b27523/target_genomes_gtdb.txt --output OceanDNA-b27523/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:16:42,415] [INFO] Task succeeded: fastANI
[2023-03-18 09:16:42,433] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:16:42,434] [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_002285415.1	s__Actibacterium pelagium	77.4361	123	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900302455.1	s__Ruegeria_E mediterranea	77.3879	115	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_004360145.1	s__Aliiroseovarius marinus	77.2561	129	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	77.1271	122	801	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_017743975.1	s__Ruegeria sp017743975	77.125	112	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003355.1	s__Donghicola tyrosinivorans	77.1136	109	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	77.093	134	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	77.0293	105	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	77.0188	116	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_001458175.1	s__Shimia marina	76.9156	99	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_000814005.1	s__Ruegeria sp000814005	76.9029	99	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	76.8181	137	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.7727	133	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032455.1	s__Ruegeria atlantica_B	76.7489	115	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.37	96.74	0.95	0.90	3	-
GCF_002358085.1	s__Thioclava arenosa	76.7032	75	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001238295.1	s__Ruegeria sp001238295	76.6427	109	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	76.6088	123	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_000203975.2	s__Leisingera sp000203975	76.6062	115	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_013032505.1	s__Ruegeria atlantica_F	76.5966	120	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	76.5695	114	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940525.2	s__Thioclava nitratireducens	76.5609	79	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
GCF_900115865.1	s__Donghicola eburneus	76.5296	110	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	99.41	99.41	0.91	0.91	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.5199	90	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	76.48	83	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	76.4471	127	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	76.4254	94	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.3577	78	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	76.3184	90	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_003201935.1	s__Yoonia sp003201935	76.3096	86	801	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	76.2812	88	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.2391	85	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900109035.1	s__Cribrihabitans marinus	76.2328	93	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900172295.1	s__Roseovarius litorisediminis	76.1534	95	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601345.1	s__Roseovarius gahaiensis	75.9826	78	801	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:16:42,434] [INFO] GTDB search result was written to OceanDNA-b27523/result_gtdb.tsv
[2023-03-18 09:16:42,434] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:16:42,438] [INFO] DFAST_QC result json was written to OceanDNA-b27523/dqc_result.json
[2023-03-18 09:16:42,438] [INFO] DFAST_QC completed!
[2023-03-18 09:16:42,438] [INFO] Total running time: 0h1m42s