[2023-03-17 04:15:14,740] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference
[2023-03-17 04:15:16,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,099] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,099] [INFO] Running command: cat /var/lib/cwl/stg6de119e6-a6c8-4837-b7a1-ddd61f915b53/OceanDNA-b28550.fa | prodigal -d OceanDNA-b28550/cds.fna -a OceanDNA-b28550/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:37,184] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:37,184] [INFO] Task started: HMMsearch
[2023-03-17 04:15:37,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b28550/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/reference_markers.hmm OceanDNA-b28550/protein.faa > /dev/null
[2023-03-17 04:15:37,443] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:37,444] [INFO] Found 6/6 markers.
[2023-03-17 04:15:37,464] [INFO] Query marker FASTA was written to OceanDNA-b28550/markers.fasta
[2023-03-17 04:15:37,465] [INFO] Task started: Blastn
[2023-03-17 04:15:37,465] [INFO] Running command: blastn -query OceanDNA-b28550/markers.fasta -db /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/reference_markers.fasta -out OceanDNA-b28550/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:38,185] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:38,186] [INFO] Selected 32 target genomes.
[2023-03-17 04:15:38,186] [INFO] Target genome list was writen to OceanDNA-b28550/target_genomes.txt
[2023-03-17 04:15:38,202] [INFO] Task started: fastANI
[2023-03-17 04:15:38,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de119e6-a6c8-4837-b7a1-ddd61f915b53/OceanDNA-b28550.fa --refList OceanDNA-b28550/target_genomes.txt --output OceanDNA-b28550/fastani_result.tsv --threads 1
[2023-03-17 04:16:00,297] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:00,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:16:00,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:16:00,314] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:16:00,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:16:00,314] [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
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	77.3592	284	1036	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	77.0425	227	1036	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.0118	234	1036	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.9627	209	1036	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.9503	210	1036	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.9348	219	1036	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.9005	222	1036	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	76.8864	154	1036	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.869	174	1036	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	76.8122	233	1036	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.8081	202	1036	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.7996	165	1036	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.7529	159	1036	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.7474	192	1036	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.6119	134	1036	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.5667	142	1036	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.5657	99	1036	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.5163	131	1036	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	76.4654	133	1036	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.4324	136	1036	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.369	153	1036	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.3638	113	1036	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	76.3521	124	1036	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.3371	180	1036	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	76.326	146	1036	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	76.3128	151	1036	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	76.2964	153	1036	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	76.2592	123	1036	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2054	148	1036	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.0924	99	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:16:00,314] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28550/tc_result.tsv
[2023-03-17 04:16:00,314] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:16:00,315] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:16:00,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/checkm_data
[2023-03-17 04:16:00,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:16:00,320] [INFO] Task started: CheckM
[2023-03-17 04:16:00,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28550/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28550/checkm_input OceanDNA-b28550/checkm_result
[2023-03-17 04:16:54,625] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:54,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:54,739] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:54,739] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:54,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28550/markers.fasta)
[2023-03-17 04:16:54,739] [INFO] Task started: Blastn
[2023-03-17 04:16:54,739] [INFO] Running command: blastn -query OceanDNA-b28550/markers.fasta -db /var/lib/cwl/stg7ebe04e6-ffd6-43d3-9000-57ebde1dec12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28550/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:55,974] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:56,182] [INFO] Selected 26 target genomes.
[2023-03-17 04:16:56,182] [INFO] Target genome list was writen to OceanDNA-b28550/target_genomes_gtdb.txt
[2023-03-17 04:16:56,332] [INFO] Task started: fastANI
[2023-03-17 04:16:56,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de119e6-a6c8-4837-b7a1-ddd61f915b53/OceanDNA-b28550.fa --refList OceanDNA-b28550/target_genomes_gtdb.txt --output OceanDNA-b28550/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:17:12,755] [INFO] Task succeeded: fastANI
[2023-03-17 04:17:12,769] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:17:12,770] [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_008065155.1	s__SW4 sp002732825	80.621	659	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	77.3305	287	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	77.0118	234	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	76.9903	210	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.9466	218	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_004145845.1	s__Marivivens sp004145845	76.8958	225	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.8955	200	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001420005.1	s__Loktanella sp001420005	76.8845	187	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.8457	220	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	76.813	164	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_900115165.1	s__Roseovarius lutimaris	76.8103	203	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	76.7673	158	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.7387	177	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	76.7374	143	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_900110705.1	s__Loktanella sp900110705	76.7253	183	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	76.6119	134	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	76.5698	143	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009363655.1	s__Roseovarius sp009363655	76.4922	124	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_000152805.1	s__Maritimibacter alkaliphilus	76.4856	133	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCA_003533975.1	s__Octadecabacter sp003533975	76.3729	120	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	76.3659	142	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002917925.1	s__Roseovarius confluentis	76.3487	120	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_002094885.1	s__Salibaculum halophilum	76.3382	125	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259905.1	s__Salipiger aestuarii	76.3167	152	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	-
GCA_002400675.1	s__NORP181 sp002400675	76.2987	98	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__NORP181	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	76.0136	123	1036	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:17:12,770] [INFO] GTDB search result was written to OceanDNA-b28550/result_gtdb.tsv
[2023-03-17 04:17:12,770] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:17:12,773] [INFO] DFAST_QC result json was written to OceanDNA-b28550/dqc_result.json
[2023-03-17 04:17:12,773] [INFO] DFAST_QC completed!
[2023-03-17 04:17:12,773] [INFO] Total running time: 0h1m58s