[2023-03-19 04:46:13,847] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:13,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:13,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference
[2023-03-19 04:46:14,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:14,956] [INFO] Task started: Prodigal
[2023-03-19 04:46:14,956] [INFO] Running command: cat /var/lib/cwl/stgd8b973fb-a4f3-412a-b6ad-40545d3d092c/OceanDNA-b28232.fa | prodigal -d OceanDNA-b28232/cds.fna -a OceanDNA-b28232/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:37,361] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:37,361] [INFO] Task started: HMMsearch
[2023-03-19 04:46:37,361] [INFO] Running command: hmmsearch --tblout OceanDNA-b28232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/reference_markers.hmm OceanDNA-b28232/protein.faa > /dev/null
[2023-03-19 04:46:37,565] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:37,566] [INFO] Found 6/6 markers.
[2023-03-19 04:46:37,587] [INFO] Query marker FASTA was written to OceanDNA-b28232/markers.fasta
[2023-03-19 04:46:37,589] [INFO] Task started: Blastn
[2023-03-19 04:46:37,589] [INFO] Running command: blastn -query OceanDNA-b28232/markers.fasta -db /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/reference_markers.fasta -out OceanDNA-b28232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:38,272] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:38,273] [INFO] Selected 32 target genomes.
[2023-03-19 04:46:38,273] [INFO] Target genome list was writen to OceanDNA-b28232/target_genomes.txt
[2023-03-19 04:46:38,296] [INFO] Task started: fastANI
[2023-03-19 04:46:38,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b973fb-a4f3-412a-b6ad-40545d3d092c/OceanDNA-b28232.fa --refList OceanDNA-b28232/target_genomes.txt --output OceanDNA-b28232/fastani_result.tsv --threads 1
[2023-03-19 04:46:59,978] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:59,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:59,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:59,996] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:59,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:46:59,996] [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
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	78.1894	324	1148	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.1815	360	1148	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.1548	393	1148	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.1508	327	1148	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1296	402	1148	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.0424	375	1148	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.9768	326	1148	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.9738	343	1148	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.9705	362	1148	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.81	306	1148	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.7436	335	1148	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.7205	299	1148	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.6969	309	1148	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.6167	291	1148	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5664	254	1148	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.5389	294	1148	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.5307	320	1148	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	77.5155	297	1148	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.5085	266	1148	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	77.4872	304	1148	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.3532	341	1148	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.3366	336	1148	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.3294	249	1148	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.2915	344	1148	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.2718	344	1148	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.2444	343	1148	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.1798	234	1148	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.1062	249	1148	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.0682	284	1148	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.0582	284	1148	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.0322	212	1148	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	76.7914	213	1148	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:46:59,997] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28232/tc_result.tsv
[2023-03-19 04:46:59,997] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:59,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:59,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/checkm_data
[2023-03-19 04:46:59,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:47:00,004] [INFO] Task started: CheckM
[2023-03-19 04:47:00,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28232/checkm_input OceanDNA-b28232/checkm_result
[2023-03-19 04:47:56,004] [INFO] Task succeeded: CheckM
[2023-03-19 04:47:56,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:47:56,026] [INFO] ===== Completeness check finished =====
[2023-03-19 04:47:56,026] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:47:56,026] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28232/markers.fasta)
[2023-03-19 04:47:56,028] [INFO] Task started: Blastn
[2023-03-19 04:47:56,028] [INFO] Running command: blastn -query OceanDNA-b28232/markers.fasta -db /var/lib/cwl/stg318d1dc4-7c1c-4b56-8e18-012998435414/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:47:57,137] [INFO] Task succeeded: Blastn
[2023-03-19 04:47:57,141] [INFO] Selected 31 target genomes.
[2023-03-19 04:47:57,141] [INFO] Target genome list was writen to OceanDNA-b28232/target_genomes_gtdb.txt
[2023-03-19 04:47:57,173] [INFO] Task started: fastANI
[2023-03-19 04:47:57,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b973fb-a4f3-412a-b6ad-40545d3d092c/OceanDNA-b28232.fa --refList OceanDNA-b28232/target_genomes_gtdb.txt --output OceanDNA-b28232/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:48:19,579] [INFO] Task succeeded: fastANI
[2023-03-19 04:48:19,594] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:48:19,594] [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_001650895.1	s__EhC02 sp001650895	81.8398	712	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282555.1	s__EhC02 sp002282555	81.7518	348	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.6619	478	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000526275.1	s__Lutimaribacter sp000526275	78.5658	475	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.1277	396	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.1203	403	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_004799325.1	s__Thalassobius vesicularis	78.0616	374	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.0138	378	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	77.8035	306	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.7935	329	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.791	308	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.7738	332	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.7407	336	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	77.6953	309	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.5843	317	1148	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_000590925.1	s__Roseicyclus elongatus	77.5558	255	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	77.5286	295	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142625.1	s__Roseovarius marisflavi	77.5155	297	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	77.4863	316	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	77.4841	305	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	77.4749	269	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003053725.1	s__Rhodovulum kholense	77.3346	300	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	77.328	338	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_008728195.1	s__Roseovarius indicus	77.2719	344	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.2452	330	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	77.2058	259	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	77.1768	246	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.0148	213	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:48:19,595] [INFO] GTDB search result was written to OceanDNA-b28232/result_gtdb.tsv
[2023-03-19 04:48:19,595] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:48:19,598] [INFO] DFAST_QC result json was written to OceanDNA-b28232/dqc_result.json
[2023-03-19 04:48:19,598] [INFO] DFAST_QC completed!
[2023-03-19 04:48:19,598] [INFO] Total running time: 0h2m6s