[2023-03-16 05:41:22,590] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:41:22,590] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:41:22,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference
[2023-03-16 05:41:23,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:41:23,681] [INFO] Task started: Prodigal
[2023-03-16 05:41:23,681] [INFO] Running command: cat /var/lib/cwl/stgf8bde933-f887-4582-b44b-fbf3f67a1407/OceanDNA-b30678.fa | prodigal -d OceanDNA-b30678/cds.fna -a OceanDNA-b30678/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:41:41,324] [INFO] Task succeeded: Prodigal
[2023-03-16 05:41:41,325] [INFO] Task started: HMMsearch
[2023-03-16 05:41:41,325] [INFO] Running command: hmmsearch --tblout OceanDNA-b30678/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/reference_markers.hmm OceanDNA-b30678/protein.faa > /dev/null
[2023-03-16 05:41:41,504] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:41:41,505] [INFO] Found 6/6 markers.
[2023-03-16 05:41:41,522] [INFO] Query marker FASTA was written to OceanDNA-b30678/markers.fasta
[2023-03-16 05:41:41,523] [INFO] Task started: Blastn
[2023-03-16 05:41:41,523] [INFO] Running command: blastn -query OceanDNA-b30678/markers.fasta -db /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/reference_markers.fasta -out OceanDNA-b30678/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:42,121] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:42,122] [INFO] Selected 28 target genomes.
[2023-03-16 05:41:42,122] [INFO] Target genome list was writen to OceanDNA-b30678/target_genomes.txt
[2023-03-16 05:41:42,136] [INFO] Task started: fastANI
[2023-03-16 05:41:42,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8bde933-f887-4582-b44b-fbf3f67a1407/OceanDNA-b30678.fa --refList OceanDNA-b30678/target_genomes.txt --output OceanDNA-b30678/fastani_result.tsv --threads 1
[2023-03-16 05:41:58,606] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:58,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:41:58,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:41:58,621] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:41:58,621] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:41:58,621] [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
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.6054	194	912	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.5941	251	912	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.5787	240	912	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	77.2892	152	912	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	77.2788	156	912	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.0926	235	912	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.9989	186	912	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.9546	179	912	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.9546	179	912	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.8932	161	912	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.8833	206	912	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.6953	171	912	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.6819	98	912	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.68	132	912	95	below_threshold
Litoreibacter halocynthiae	strain=DSM 29467	GCA_004365635.1	1242689	1242689	type	True	76.6476	142	912	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.6219	99	912	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.5653	141	912	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.4934	86	912	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.3227	105	912	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	76.3224	102	912	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2986	159	912	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.2921	160	912	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.9808	72	912	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	75.8932	92	912	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.715	73	912	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	75.7119	85	912	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	75.5602	52	912	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	75.521	54	912	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:41:58,622] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30678/tc_result.tsv
[2023-03-16 05:41:58,622] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:41:58,622] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:41:58,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/checkm_data
[2023-03-16 05:41:58,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:41:58,645] [INFO] Task started: CheckM
[2023-03-16 05:41:58,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30678/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30678/checkm_input OceanDNA-b30678/checkm_result
[2023-03-16 05:42:45,213] [INFO] Task succeeded: CheckM
[2023-03-16 05:42:45,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:42:45,216] [INFO] ===== Completeness check finished =====
[2023-03-16 05:42:45,216] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:42:45,216] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30678/markers.fasta)
[2023-03-16 05:42:45,218] [INFO] Task started: Blastn
[2023-03-16 05:42:45,218] [INFO] Running command: blastn -query OceanDNA-b30678/markers.fasta -db /var/lib/cwl/stgd8850385-9165-4e9d-b4d9-def39e39307d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30678/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:42:46,087] [INFO] Task succeeded: Blastn
[2023-03-16 05:42:46,088] [INFO] Selected 23 target genomes.
[2023-03-16 05:42:46,088] [INFO] Target genome list was writen to OceanDNA-b30678/target_genomes_gtdb.txt
[2023-03-16 05:42:46,118] [INFO] Task started: fastANI
[2023-03-16 05:42:46,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8bde933-f887-4582-b44b-fbf3f67a1407/OceanDNA-b30678.fa --refList OceanDNA-b30678/target_genomes_gtdb.txt --output OceanDNA-b30678/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:43:00,756] [INFO] Task succeeded: fastANI
[2023-03-16 05:43:00,769] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:43:00,769] [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	81.0984	485	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCA_905182645.1	s__Yoonia sp905182645	78.7113	288	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318235.1	s__Yoonia sp003318235	77.631	200	912	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	77.6054	194	912	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	77.5732	239	912	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	77.5663	205	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854415.1	s__Yoonia sp017854415	77.4535	202	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	77.3465	193	912	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	77.2184	231	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.1336	229	912	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	77.0926	235	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCA_018402175.1	s__Yoonia sp018402175	77.0881	189	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_002797915.1	s__Yoonia maricola	76.9989	186	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058085.1	s__Yoonia sediminilitoris	76.9546	179	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114675.1	s__Yoonia litorea	76.8932	161	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	76.6291	99	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	76.6219	99	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_001420005.1	s__Loktanella sp001420005	76.3856	162	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106805.1	s__Ruegeria halocynthiae	76.3224	102	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.2921	160	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.2306	151	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	75.7684	62	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_900005615.1	s__Paracoccus aminovorans	75.5425	53	912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:43:00,769] [INFO] GTDB search result was written to OceanDNA-b30678/result_gtdb.tsv
[2023-03-16 05:43:00,770] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:43:00,772] [INFO] DFAST_QC result json was written to OceanDNA-b30678/dqc_result.json
[2023-03-16 05:43:00,772] [INFO] DFAST_QC completed!
[2023-03-16 05:43:00,772] [INFO] Total running time: 0h1m38s