[2023-03-15 11:24:11,464] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,465] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference
[2023-03-15 11:24:12,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,580] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,580] [INFO] Running command: cat /var/lib/cwl/stg8f5ff4cb-de85-455f-b420-e0d7d5c947b5/OceanDNA-b30687.fa | prodigal -d OceanDNA-b30687/cds.fna -a OceanDNA-b30687/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:28,932] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:28,933] [INFO] Task started: HMMsearch
[2023-03-15 11:24:28,933] [INFO] Running command: hmmsearch --tblout OceanDNA-b30687/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/reference_markers.hmm OceanDNA-b30687/protein.faa > /dev/null
[2023-03-15 11:24:29,117] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:29,118] [INFO] Found 6/6 markers.
[2023-03-15 11:24:29,138] [INFO] Query marker FASTA was written to OceanDNA-b30687/markers.fasta
[2023-03-15 11:24:29,138] [INFO] Task started: Blastn
[2023-03-15 11:24:29,138] [INFO] Running command: blastn -query OceanDNA-b30687/markers.fasta -db /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/reference_markers.fasta -out OceanDNA-b30687/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:29,822] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:29,823] [INFO] Selected 33 target genomes.
[2023-03-15 11:24:29,823] [INFO] Target genome list was writen to OceanDNA-b30687/target_genomes.txt
[2023-03-15 11:24:29,838] [INFO] Task started: fastANI
[2023-03-15 11:24:29,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5ff4cb-de85-455f-b420-e0d7d5c947b5/OceanDNA-b30687.fa --refList OceanDNA-b30687/target_genomes.txt --output OceanDNA-b30687/fastani_result.tsv --threads 1
[2023-03-15 11:24:49,691] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:49,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:49,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:49,707] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:49,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:24:49,708] [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
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.5281	181	854	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.4348	81	854	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.3968	111	854	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.3903	151	854	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.3702	111	854	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.3671	98	854	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.3544	124	854	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.3344	78	854	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.3146	90	854	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	76.2839	113	854	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	76.2839	113	854	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.2718	136	854	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.2172	99	854	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1142	89	854	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	76.1079	98	854	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.0622	86	854	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	76.0381	73	854	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	75.9985	75	854	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	75.996	92	854	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.992	83	854	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	75.9841	59	854	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	75.9686	88	854	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	75.9656	81	854	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	75.9548	96	854	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	75.9514	89	854	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.9514	89	854	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	75.8945	110	854	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.8772	77	854	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	75.8671	79	854	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	75.7922	89	854	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	75.7562	86	854	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	75.5305	67	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:49,708] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30687/tc_result.tsv
[2023-03-15 11:24:49,708] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:49,708] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:49,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/checkm_data
[2023-03-15 11:24:49,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:49,714] [INFO] Task started: CheckM
[2023-03-15 11:24:49,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30687/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30687/checkm_input OceanDNA-b30687/checkm_result
[2023-03-15 11:25:33,098] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:33,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:33,102] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:33,103] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:33,103] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30687/markers.fasta)
[2023-03-15 11:25:33,104] [INFO] Task started: Blastn
[2023-03-15 11:25:33,104] [INFO] Running command: blastn -query OceanDNA-b30687/markers.fasta -db /var/lib/cwl/stg5b89ce70-a725-416a-905a-7396b95ed720/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30687/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:34,356] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:34,357] [INFO] Selected 28 target genomes.
[2023-03-15 11:25:34,357] [INFO] Target genome list was writen to OceanDNA-b30687/target_genomes_gtdb.txt
[2023-03-15 11:25:34,414] [INFO] Task started: fastANI
[2023-03-15 11:25:34,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5ff4cb-de85-455f-b420-e0d7d5c947b5/OceanDNA-b30687.fa --refList OceanDNA-b30687/target_genomes_gtdb.txt --output OceanDNA-b30687/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:52,617] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:52,632] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:25:52,632] [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_002430125.1	s__UBA5972 sp002430125	78.767	333	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	99.40	99.40	0.79	0.79	2	-
GCA_013151535.1	s__UBA5972 sp013151535	77.151	261	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151335.1	s__UBA5972 sp013151335	76.9526	188	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487165.1	s__UBA5972 sp015487165	76.8596	179	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.7271	123	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	76.6001	114	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719615.1	s__Amylibacter sediminis	76.5599	122	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001730095.1	s__Leisingera sp001730095	76.396	85	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.38	112	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002751875.1	s__Oceaniglobus indicus	76.3136	102	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.3012	121	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.2241	87	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643735.1	s__Amylibacter cionae	76.1398	114	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	76.123	115	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCA_018223125.1	s__Amylibacter sp018223125	76.1218	119	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110285.1	s__Paracoccus alcaliphilus	76.1111	98	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155295.1	s__Pseudogemmobacter sp013155295	76.0732	87	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105075.1	s__Pseudogemmobacter sp900105075	76.0689	84	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090885.1	s__NORP110 sp019090885	76.0663	91	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__NORP110	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	76.0544	89	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	76.0364	121	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_900156255.1	s__Paracoccus thiocyanatus	75.9801	93	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_002210095.1	s__Marinibacterium profundimaris	75.9648	95	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405985.1	s__Pseudogemmobacter sp016405985	75.9315	93	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265325.1	s__Halovulum sediminis	75.7517	83	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	75.742	86	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622145.1	s__Paracoccus yeei	75.7405	85	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_014196795.1	s__Sagittula marina	75.5305	67	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:52,633] [INFO] GTDB search result was written to OceanDNA-b30687/result_gtdb.tsv
[2023-03-15 11:25:52,633] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:52,637] [INFO] DFAST_QC result json was written to OceanDNA-b30687/dqc_result.json
[2023-03-15 11:25:52,637] [INFO] DFAST_QC completed!
[2023-03-15 11:25:52,637] [INFO] Total running time: 0h1m41s