[2023-03-18 21:03:43,551] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:03:43,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:03:43,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference
[2023-03-18 21:03:44,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:03:44,648] [INFO] Task started: Prodigal
[2023-03-18 21:03:44,648] [INFO] Running command: cat /var/lib/cwl/stg072569ea-eb2a-4ebd-82d6-6c4ebc3bcec0/OceanDNA-b28155.fa | prodigal -d OceanDNA-b28155/cds.fna -a OceanDNA-b28155/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:03:57,116] [INFO] Task succeeded: Prodigal
[2023-03-18 21:03:57,117] [INFO] Task started: HMMsearch
[2023-03-18 21:03:57,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b28155/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/reference_markers.hmm OceanDNA-b28155/protein.faa > /dev/null
[2023-03-18 21:03:57,293] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:03:57,293] [INFO] Found 6/6 markers.
[2023-03-18 21:03:57,318] [INFO] Query marker FASTA was written to OceanDNA-b28155/markers.fasta
[2023-03-18 21:03:57,319] [INFO] Task started: Blastn
[2023-03-18 21:03:57,319] [INFO] Running command: blastn -query OceanDNA-b28155/markers.fasta -db /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/reference_markers.fasta -out OceanDNA-b28155/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:03:58,007] [INFO] Task succeeded: Blastn
[2023-03-18 21:03:58,012] [INFO] Selected 27 target genomes.
[2023-03-18 21:03:58,012] [INFO] Target genome list was writen to OceanDNA-b28155/target_genomes.txt
[2023-03-18 21:03:58,022] [INFO] Task started: fastANI
[2023-03-18 21:03:58,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg072569ea-eb2a-4ebd-82d6-6c4ebc3bcec0/OceanDNA-b28155.fa --refList OceanDNA-b28155/target_genomes.txt --output OceanDNA-b28155/fastani_result.tsv --threads 1
[2023-03-18 21:04:16,420] [INFO] Task succeeded: fastANI
[2023-03-18 21:04:16,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:04:16,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:04:16,434] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:04:16,434] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:04:16,435] [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
Cognatiyoonia sediminum	strain=DSM 28715	GCA_900129845.1	1508389	1508389	type	True	78.7007	257	613	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.6806	96	613	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.6537	96	613	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.5951	119	613	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	76.585	103	613	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.4977	88	613	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.4656	82	613	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.4606	86	613	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.449	101	613	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.414	88	613	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.3793	65	613	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.3686	110	613	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.2901	83	613	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.2683	84	613	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2617	94	613	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.2427	110	613	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.2142	75	613	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	76.1738	78	613	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.1695	78	613	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.0986	111	613	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	75.995	90	613	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.9394	67	613	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	75.8886	92	613	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.7149	55	613	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	75.5821	67	613	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:04:16,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28155/tc_result.tsv
[2023-03-18 21:04:16,437] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:04:16,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:04:16,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/checkm_data
[2023-03-18 21:04:16,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:04:16,501] [INFO] Task started: CheckM
[2023-03-18 21:04:16,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28155/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28155/checkm_input OceanDNA-b28155/checkm_result
[2023-03-18 21:04:51,442] [INFO] Task succeeded: CheckM
[2023-03-18 21:04:51,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:04:51,449] [INFO] ===== Completeness check finished =====
[2023-03-18 21:04:51,449] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:04:51,449] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28155/markers.fasta)
[2023-03-18 21:04:51,450] [INFO] Task started: Blastn
[2023-03-18 21:04:51,450] [INFO] Running command: blastn -query OceanDNA-b28155/markers.fasta -db /var/lib/cwl/stg2311d3a3-3143-4d2c-8256-ae909c56d483/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28155/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:04:52,640] [INFO] Task succeeded: Blastn
[2023-03-18 21:04:52,643] [INFO] Selected 28 target genomes.
[2023-03-18 21:04:52,643] [INFO] Target genome list was writen to OceanDNA-b28155/target_genomes_gtdb.txt
[2023-03-18 21:04:52,670] [INFO] Task started: fastANI
[2023-03-18 21:04:52,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg072569ea-eb2a-4ebd-82d6-6c4ebc3bcec0/OceanDNA-b28155.fa --refList OceanDNA-b28155/target_genomes_gtdb.txt --output OceanDNA-b28155/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:05:08,657] [INFO] Task succeeded: fastANI
[2023-03-18 21:05:08,672] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:05:08,672] [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
GCF_900129845.1	s__Cognatiyoonia sediminum	78.7007	257	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	76.7373	124	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.6626	67	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	76.5951	119	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	76.5575	77	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.4699	106	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.4674	129	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	76.4544	125	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	76.449	101	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	76.4426	120	613	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	76.4073	120	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	76.3327	110	613	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	76.2966	145	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	76.2951	88	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCA_014859355.1	s__Yoonia sp014859355	76.2893	102	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	76.2481	81	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	76.2217	89	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	76.2124	68	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCA_009920775.1	s__Marivivens sp009920775	76.1909	75	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	76.1123	110	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854415.1	s__Yoonia sp017854415	76.0616	82	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155735.2	s__Octadecabacter arcticus	75.995	90	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_900156805.1	s__Roseivivax lentus	75.8886	92	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	75.872	89	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	75.737	72	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760615.1	s__Puniceibacterium antarcticum	75.5821	67	613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:05:08,674] [INFO] GTDB search result was written to OceanDNA-b28155/result_gtdb.tsv
[2023-03-18 21:05:08,676] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:05:08,682] [INFO] DFAST_QC result json was written to OceanDNA-b28155/dqc_result.json
[2023-03-18 21:05:08,682] [INFO] DFAST_QC completed!
[2023-03-18 21:05:08,683] [INFO] Total running time: 0h1m25s