[2023-03-16 10:11:21,327] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:11:21,327] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:11:21,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference
[2023-03-16 10:11:22,433] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:11:22,434] [INFO] Task started: Prodigal
[2023-03-16 10:11:22,434] [INFO] Running command: cat /var/lib/cwl/stgf7e2606f-02e2-4b1f-b536-a4103e79b099/OceanDNA-b30676.fa | prodigal -d OceanDNA-b30676/cds.fna -a OceanDNA-b30676/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:11:40,775] [INFO] Task succeeded: Prodigal
[2023-03-16 10:11:40,775] [INFO] Task started: HMMsearch
[2023-03-16 10:11:40,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b30676/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/reference_markers.hmm OceanDNA-b30676/protein.faa > /dev/null
[2023-03-16 10:11:40,942] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:11:40,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf7e2606f-02e2-4b1f-b536-a4103e79b099/OceanDNA-b30676.fa]
[2023-03-16 10:11:40,960] [INFO] Query marker FASTA was written to OceanDNA-b30676/markers.fasta
[2023-03-16 10:11:40,961] [INFO] Task started: Blastn
[2023-03-16 10:11:40,961] [INFO] Running command: blastn -query OceanDNA-b30676/markers.fasta -db /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/reference_markers.fasta -out OceanDNA-b30676/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:11:41,586] [INFO] Task succeeded: Blastn
[2023-03-16 10:11:41,587] [INFO] Selected 26 target genomes.
[2023-03-16 10:11:41,587] [INFO] Target genome list was writen to OceanDNA-b30676/target_genomes.txt
[2023-03-16 10:11:41,603] [INFO] Task started: fastANI
[2023-03-16 10:11:41,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e2606f-02e2-4b1f-b536-a4103e79b099/OceanDNA-b30676.fa --refList OceanDNA-b30676/target_genomes.txt --output OceanDNA-b30676/fastani_result.tsv --threads 1
[2023-03-16 10:11:56,982] [INFO] Task succeeded: fastANI
[2023-03-16 10:11:56,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:11:56,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:11:56,997] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:11:56,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:11:56,997] [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	77.317	194	944	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.2588	141	944	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.0572	193	944	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.0069	206	944	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	77.0021	134	944	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.5902	169	944	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.4968	136	944	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.4141	106	944	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	76.3988	92	944	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.3869	172	944	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.3869	172	944	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3519	138	944	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3377	139	944	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	76.3251	95	944	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.1919	77	944	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	76.1874	90	944	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.1317	103	944	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.1085	78	944	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	76.0437	77	944	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	75.9813	95	944	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	75.9513	116	944	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	75.8878	80	944	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	75.7585	76	944	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.7299	56	944	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.7213	66	944	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	75.7213	66	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:11:56,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30676/tc_result.tsv
[2023-03-16 10:11:56,998] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:11:56,998] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:11:56,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/checkm_data
[2023-03-16 10:11:56,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:11:57,121] [INFO] Task started: CheckM
[2023-03-16 10:11:57,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30676/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30676/checkm_input OceanDNA-b30676/checkm_result
[2023-03-16 10:12:44,234] [INFO] Task succeeded: CheckM
[2023-03-16 10:12:44,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:12:44,237] [INFO] ===== Completeness check finished =====
[2023-03-16 10:12:44,237] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:12:44,237] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30676/markers.fasta)
[2023-03-16 10:12:44,238] [INFO] Task started: Blastn
[2023-03-16 10:12:44,238] [INFO] Running command: blastn -query OceanDNA-b30676/markers.fasta -db /var/lib/cwl/stg7c542c96-0b36-473b-b637-be9b2e317ced/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30676/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:12:45,242] [INFO] Task succeeded: Blastn
[2023-03-16 10:12:45,243] [INFO] Selected 19 target genomes.
[2023-03-16 10:12:45,243] [INFO] Target genome list was writen to OceanDNA-b30676/target_genomes_gtdb.txt
[2023-03-16 10:12:45,324] [INFO] Task started: fastANI
[2023-03-16 10:12:45,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e2606f-02e2-4b1f-b536-a4103e79b099/OceanDNA-b30676.fa --refList OceanDNA-b30676/target_genomes_gtdb.txt --output OceanDNA-b30676/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:12:56,936] [INFO] Task succeeded: fastANI
[2023-03-16 10:12:56,947] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:12:56,948] [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	79.1966	383	944	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	78.0155	271	944	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	77.3499	160	944	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	77.317	194	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.0069	206	944	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	76.9706	188	944	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	76.9258	188	944	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	76.7547	161	944	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	76.5772	170	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.5538	126	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.4968	136	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	76.3793	110	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_001650895.1	s__EhC02 sp001650895	76.376	84	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.3377	139	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_009857745.1	s__Thalassobius mangrovi	76.2679	92	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	76.2088	119	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	76.1874	90	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	76.1317	103	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_900129875.1	s__Marivita hallyeonensis	75.7585	76	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:12:56,948] [INFO] GTDB search result was written to OceanDNA-b30676/result_gtdb.tsv
[2023-03-16 10:12:56,948] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:12:56,951] [INFO] DFAST_QC result json was written to OceanDNA-b30676/dqc_result.json
[2023-03-16 10:12:56,951] [INFO] DFAST_QC completed!
[2023-03-16 10:12:56,951] [INFO] Total running time: 0h1m36s