[2023-03-18 10:12:10,235] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,235] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,235] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference
[2023-03-18 10:12:11,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,374] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,374] [INFO] Running command: cat /var/lib/cwl/stg61897d67-987e-4ea6-b93f-802b9d20645f/OceanDNA-b30685.fa | prodigal -d OceanDNA-b30685/cds.fna -a OceanDNA-b30685/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:27,270] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:27,270] [INFO] Task started: HMMsearch
[2023-03-18 10:12:27,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b30685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/reference_markers.hmm OceanDNA-b30685/protein.faa > /dev/null
[2023-03-18 10:12:27,446] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:27,447] [INFO] Found 6/6 markers.
[2023-03-18 10:12:27,470] [INFO] Query marker FASTA was written to OceanDNA-b30685/markers.fasta
[2023-03-18 10:12:27,471] [INFO] Task started: Blastn
[2023-03-18 10:12:27,471] [INFO] Running command: blastn -query OceanDNA-b30685/markers.fasta -db /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/reference_markers.fasta -out OceanDNA-b30685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:28,161] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:28,163] [INFO] Selected 26 target genomes.
[2023-03-18 10:12:28,164] [INFO] Target genome list was writen to OceanDNA-b30685/target_genomes.txt
[2023-03-18 10:12:28,179] [INFO] Task started: fastANI
[2023-03-18 10:12:28,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg61897d67-987e-4ea6-b93f-802b9d20645f/OceanDNA-b30685.fa --refList OceanDNA-b30685/target_genomes.txt --output OceanDNA-b30685/fastani_result.tsv --threads 1
[2023-03-18 10:12:44,205] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:44,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:44,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:44,220] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:44,220] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:12:44,220] [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
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.4111	214	815	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.2945	167	815	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.172	190	815	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.1266	200	815	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.9915	198	815	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.8579	167	815	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.7719	162	815	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.7673	129	815	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.707	145	815	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.6158	112	815	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.5257	110	815	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.3626	84	815	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	76.3341	68	815	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	76.3328	144	815	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2337	126	815	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.2334	113	815	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.2265	128	815	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2075	102	815	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.1492	87	815	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.107	88	815	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	76.0381	79	815	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.9835	72	815	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	75.9616	88	815	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.7744	62	815	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.6913	70	815	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.6913	70	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:12:44,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30685/tc_result.tsv
[2023-03-18 10:12:44,222] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:44,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:44,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/checkm_data
[2023-03-18 10:12:44,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:44,240] [INFO] Task started: CheckM
[2023-03-18 10:12:44,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30685/checkm_input OceanDNA-b30685/checkm_result
[2023-03-18 10:13:26,875] [INFO] Task succeeded: CheckM
[2023-03-18 10:13:26,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:13:26,879] [INFO] ===== Completeness check finished =====
[2023-03-18 10:13:26,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:13:26,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30685/markers.fasta)
[2023-03-18 10:13:26,879] [INFO] Task started: Blastn
[2023-03-18 10:13:26,879] [INFO] Running command: blastn -query OceanDNA-b30685/markers.fasta -db /var/lib/cwl/stgb5ceab79-1a7a-4f06-a718-9a67d4854cfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:13:28,101] [INFO] Task succeeded: Blastn
[2023-03-18 10:13:28,102] [INFO] Selected 20 target genomes.
[2023-03-18 10:13:28,102] [INFO] Target genome list was writen to OceanDNA-b30685/target_genomes_gtdb.txt
[2023-03-18 10:13:28,141] [INFO] Task started: fastANI
[2023-03-18 10:13:28,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg61897d67-987e-4ea6-b93f-802b9d20645f/OceanDNA-b30685.fa --refList OceanDNA-b30685/target_genomes_gtdb.txt --output OceanDNA-b30685/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:13:40,177] [INFO] Task succeeded: fastANI
[2023-03-18 10:13:40,189] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:13:40,189] [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_002378665.1	s__Yoonia sp002378665	99.1444	713	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	conclusive
GCA_905182645.1	s__Yoonia sp905182645	78.5175	257	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199395.1	s__Yoonia ponticola	77.4111	214	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.2945	167	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967725.1	s__Yoonia sp000967725	77.2404	138	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	77.2209	200	815	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	77.172	190	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_003201935.1	s__Yoonia sp003201935	77.1292	196	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	77.0761	193	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933395.1	s__Yoonia maritima_A	77.0669	163	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	77.0343	198	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	76.9915	198	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_000169435.1	s__Yoonia sp000169435	76.9359	177	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859355.1	s__Yoonia sp014859355	76.9147	145	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	76.8579	167	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	76.7211	144	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	76.4776	97	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	76.2684	81	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003417655.1	s__Lentibacter sp003417655	76.0037	71	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	75.639	73	815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:13:40,190] [INFO] GTDB search result was written to OceanDNA-b30685/result_gtdb.tsv
[2023-03-18 10:13:40,190] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:13:40,192] [INFO] DFAST_QC result json was written to OceanDNA-b30685/dqc_result.json
[2023-03-18 10:13:40,193] [INFO] DFAST_QC completed!
[2023-03-18 10:13:40,193] [INFO] Total running time: 0h1m30s