[2023-03-15 08:09:45,395] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,395] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference
[2023-03-15 08:09:46,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,553] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,553] [INFO] Running command: cat /var/lib/cwl/stg7001ee68-fe1f-4c70-9b2e-f457769915a2/OceanDNA-b28160.fa | prodigal -d OceanDNA-b28160/cds.fna -a OceanDNA-b28160/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:59,251] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:59,251] [INFO] Task started: HMMsearch
[2023-03-15 08:09:59,251] [INFO] Running command: hmmsearch --tblout OceanDNA-b28160/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/reference_markers.hmm OceanDNA-b28160/protein.faa > /dev/null
[2023-03-15 08:09:59,459] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:59,459] [INFO] Found 6/6 markers.
[2023-03-15 08:09:59,479] [INFO] Query marker FASTA was written to OceanDNA-b28160/markers.fasta
[2023-03-15 08:09:59,480] [INFO] Task started: Blastn
[2023-03-15 08:09:59,480] [INFO] Running command: blastn -query OceanDNA-b28160/markers.fasta -db /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/reference_markers.fasta -out OceanDNA-b28160/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:00,081] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:00,082] [INFO] Selected 39 target genomes.
[2023-03-15 08:10:00,082] [INFO] Target genome list was writen to OceanDNA-b28160/target_genomes.txt
[2023-03-15 08:10:00,117] [INFO] Task started: fastANI
[2023-03-15 08:10:00,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg7001ee68-fe1f-4c70-9b2e-f457769915a2/OceanDNA-b28160.fa --refList OceanDNA-b28160/target_genomes.txt --output OceanDNA-b28160/fastani_result.tsv --threads 1
[2023-03-15 08:10:26,963] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:26,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:26,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:26,981] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:26,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:26,981] [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
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.9848	68	642	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	76.7291	60	642	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	76.6696	59	642	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.6617	59	642	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.6597	60	642	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.6389	69	642	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.6288	59	642	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.6074	55	642	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.4599	63	642	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4346	61	642	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.3444	53	642	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.3407	62	642	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	76.2463	58	642	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	76.2148	59	642	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.2148	59	642	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	76.0964	50	642	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.0959	60	642	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	76.043	50	642	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.043	50	642	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	75.9795	54	642	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	75.9067	77	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:26,982] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28160/tc_result.tsv
[2023-03-15 08:10:26,982] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:26,982] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:26,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/checkm_data
[2023-03-15 08:10:26,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:26,988] [INFO] Task started: CheckM
[2023-03-15 08:10:26,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28160/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28160/checkm_input OceanDNA-b28160/checkm_result
[2023-03-15 08:11:02,684] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:02,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:02,687] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:02,688] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:02,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28160/markers.fasta)
[2023-03-15 08:11:02,689] [INFO] Task started: Blastn
[2023-03-15 08:11:02,689] [INFO] Running command: blastn -query OceanDNA-b28160/markers.fasta -db /var/lib/cwl/stg6eeedc90-1ef8-4e17-a67b-0c01219cbcf1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28160/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:03,671] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:03,672] [INFO] Selected 32 target genomes.
[2023-03-15 08:11:03,672] [INFO] Target genome list was writen to OceanDNA-b28160/target_genomes_gtdb.txt
[2023-03-15 08:11:03,704] [INFO] Task started: fastANI
[2023-03-15 08:11:03,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg7001ee68-fe1f-4c70-9b2e-f457769915a2/OceanDNA-b28160.fa --refList OceanDNA-b28160/target_genomes_gtdb.txt --output OceanDNA-b28160/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:23,240] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:23,253] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:11:23,253] [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_017643385.1	s__Dinoroseobacter sp013215265	98.2597	630	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	98.60	98.60	0.93	0.93	2	conclusive
GCF_005938225.1	s__Arenibacterium halophilum	76.6984	60	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_014656375.1	s__Aliiroseovarius zhejiangensis	76.6597	60	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.6288	59	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	76.6074	55	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	76.6011	64	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.435	53	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.3745	59	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844665.1	s__Dinoroseobacter sp006844665	76.3721	75	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651375.1	s__Tateyamaria omphalii	76.3697	61	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001238295.1	s__Ruegeria sp001238295	76.3578	57	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.3444	53	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	76.2459	57	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	76.2428	65	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.2203	75	642	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_008728195.1	s__Roseovarius indicus	76.2148	59	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	76.2103	71	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020355.1	s__Thioclava sediminum	76.0964	50	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCA_009830125.1	s__GH1-50 sp009830125	76.0959	60	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.0803	51	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_001482405.1	s__Ponticoccus marisrubri	76.0668	66	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.0554	56	642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:23,253] [INFO] GTDB search result was written to OceanDNA-b28160/result_gtdb.tsv
[2023-03-15 08:11:23,254] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:23,256] [INFO] DFAST_QC result json was written to OceanDNA-b28160/dqc_result.json
[2023-03-15 08:11:23,256] [INFO] DFAST_QC completed!
[2023-03-15 08:11:23,256] [INFO] Total running time: 0h1m38s