[2023-03-16 11:37:45,342] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:37:45,343] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:37:45,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference
[2023-03-16 11:37:47,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:37:47,976] [INFO] Task started: Prodigal
[2023-03-16 11:37:47,976] [INFO] Running command: cat /var/lib/cwl/stgd66b8aa4-d1ed-4435-bc51-a446e5dd5fa3/OceanDNA-b30712.fa | prodigal -d OceanDNA-b30712/cds.fna -a OceanDNA-b30712/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:38:04,050] [INFO] Task succeeded: Prodigal
[2023-03-16 11:38:04,051] [INFO] Task started: HMMsearch
[2023-03-16 11:38:04,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b30712/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/reference_markers.hmm OceanDNA-b30712/protein.faa > /dev/null
[2023-03-16 11:38:04,221] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:38:04,221] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd66b8aa4-d1ed-4435-bc51-a446e5dd5fa3/OceanDNA-b30712.fa]
[2023-03-16 11:38:04,238] [INFO] Query marker FASTA was written to OceanDNA-b30712/markers.fasta
[2023-03-16 11:38:04,239] [INFO] Task started: Blastn
[2023-03-16 11:38:04,239] [INFO] Running command: blastn -query OceanDNA-b30712/markers.fasta -db /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/reference_markers.fasta -out OceanDNA-b30712/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:38:04,987] [INFO] Task succeeded: Blastn
[2023-03-16 11:38:04,988] [INFO] Selected 26 target genomes.
[2023-03-16 11:38:04,989] [INFO] Target genome list was writen to OceanDNA-b30712/target_genomes.txt
[2023-03-16 11:38:05,002] [INFO] Task started: fastANI
[2023-03-16 11:38:05,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66b8aa4-d1ed-4435-bc51-a446e5dd5fa3/OceanDNA-b30712.fa --refList OceanDNA-b30712/target_genomes.txt --output OceanDNA-b30712/fastani_result.tsv --threads 1
[2023-03-16 11:38:21,587] [INFO] Task succeeded: fastANI
[2023-03-16 11:38:21,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:38:21,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:38:21,603] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:38:21,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:38:21,604] [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 vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	87.3539	515	583	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	78.4423	322	583	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.9908	269	583	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.9638	278	583	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.7081	258	583	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.7081	258	583	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.6485	234	583	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.646	243	583	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.5946	252	583	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.5789	214	583	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.4843	219	583	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.4825	216	583	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.459	213	583	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.4465	206	583	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.3743	222	583	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	77.2798	207	583	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.2298	231	583	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1937	208	583	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.184	215	583	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.1675	217	583	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.0725	223	583	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.9458	204	583	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.8913	149	583	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	76.7258	152	583	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.6545	190	583	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.5208	114	583	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:38:21,604] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30712/tc_result.tsv
[2023-03-16 11:38:21,604] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:38:21,604] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:38:21,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/checkm_data
[2023-03-16 11:38:21,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:38:21,608] [INFO] Task started: CheckM
[2023-03-16 11:38:21,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30712/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30712/checkm_input OceanDNA-b30712/checkm_result
[2023-03-16 11:38:54,533] [INFO] Task succeeded: CheckM
[2023-03-16 11:38:54,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:38:54,535] [INFO] ===== Completeness check finished =====
[2023-03-16 11:38:54,536] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:38:54,536] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30712/markers.fasta)
[2023-03-16 11:38:54,537] [INFO] Task started: Blastn
[2023-03-16 11:38:54,537] [INFO] Running command: blastn -query OceanDNA-b30712/markers.fasta -db /var/lib/cwl/stgf7786df6-ac71-46be-bab2-a03241c69be5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30712/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:38:55,923] [INFO] Task succeeded: Blastn
[2023-03-16 11:38:55,924] [INFO] Selected 6 target genomes.
[2023-03-16 11:38:55,924] [INFO] Target genome list was writen to OceanDNA-b30712/target_genomes_gtdb.txt
[2023-03-16 11:38:56,137] [INFO] Task started: fastANI
[2023-03-16 11:38:56,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66b8aa4-d1ed-4435-bc51-a446e5dd5fa3/OceanDNA-b30712.fa --refList OceanDNA-b30712/target_genomes_gtdb.txt --output OceanDNA-b30712/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:39:00,230] [INFO] Task succeeded: fastANI
[2023-03-16 11:39:00,235] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:39:00,235] [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_018402175.1	s__Yoonia sp018402175	98.22	544	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	conclusive
GCF_000152785.1	s__Yoonia vestfoldensis_A	94.025	559	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	89.0808	539	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	87.3539	515	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	83.2087	487	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551805.1	s__Yoonia sp003551805	82.9859	393	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-16 11:39:00,235] [INFO] GTDB search result was written to OceanDNA-b30712/result_gtdb.tsv
[2023-03-16 11:39:00,235] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:39:00,237] [INFO] DFAST_QC result json was written to OceanDNA-b30712/dqc_result.json
[2023-03-16 11:39:00,237] [INFO] DFAST_QC completed!
[2023-03-16 11:39:00,237] [INFO] Total running time: 0h1m15s