[2023-03-15 16:21:34,083] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:21:34,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:21:34,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference
[2023-03-15 16:21:36,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:21:36,305] [INFO] Task started: Prodigal
[2023-03-15 16:21:36,305] [INFO] Running command: cat /var/lib/cwl/stg467bf132-87ee-4253-bee7-5239b5ff1d16/OceanDNA-b23327.fa | prodigal -d OceanDNA-b23327/cds.fna -a OceanDNA-b23327/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:21:41,820] [INFO] Task succeeded: Prodigal
[2023-03-15 16:21:41,820] [INFO] Task started: HMMsearch
[2023-03-15 16:21:41,820] [INFO] Running command: hmmsearch --tblout OceanDNA-b23327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/reference_markers.hmm OceanDNA-b23327/protein.faa > /dev/null
[2023-03-15 16:21:41,981] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:21:41,981] [INFO] Found 6/6 markers.
[2023-03-15 16:21:42,026] [INFO] Query marker FASTA was written to OceanDNA-b23327/markers.fasta
[2023-03-15 16:21:42,028] [INFO] Task started: Blastn
[2023-03-15 16:21:42,028] [INFO] Running command: blastn -query OceanDNA-b23327/markers.fasta -db /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/reference_markers.fasta -out OceanDNA-b23327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:21:43,135] [INFO] Task succeeded: Blastn
[2023-03-15 16:21:43,144] [INFO] Selected 21 target genomes.
[2023-03-15 16:21:43,144] [INFO] Target genome list was writen to OceanDNA-b23327/target_genomes.txt
[2023-03-15 16:21:43,158] [INFO] Task started: fastANI
[2023-03-15 16:21:43,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg467bf132-87ee-4253-bee7-5239b5ff1d16/OceanDNA-b23327.fa --refList OceanDNA-b23327/target_genomes.txt --output OceanDNA-b23327/fastani_result.tsv --threads 1
[2023-03-15 16:21:53,344] [INFO] Task succeeded: fastANI
[2023-03-15 16:21:53,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:21:53,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:21:53,357] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:21:53,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:21:53,357] [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
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.0939	75	140	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.0416	95	140	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	79.9512	88	140	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	79.9311	85	140	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.8791	90	140	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	79.7554	91	140	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.5134	79	140	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	79.4627	76	140	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	79.4214	89	140	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	79.4093	92	140	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	79.3023	71	140	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.185	86	140	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	79.0838	84	140	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	79.0223	83	140	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	78.9687	84	140	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	78.9594	88	140	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	78.9353	93	140	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	78.7836	73	140	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	77.8094	56	140	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	76.8975	50	140	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:21:53,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23327/tc_result.tsv
[2023-03-15 16:21:53,360] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:21:53,360] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:21:53,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/checkm_data
[2023-03-15 16:21:53,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:21:53,441] [INFO] Task started: CheckM
[2023-03-15 16:21:53,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23327/checkm_input OceanDNA-b23327/checkm_result
[2023-03-15 16:22:13,334] [INFO] Task succeeded: CheckM
[2023-03-15 16:22:13,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:22:13,362] [INFO] ===== Completeness check finished =====
[2023-03-15 16:22:13,363] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:22:13,363] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23327/markers.fasta)
[2023-03-15 16:22:13,364] [INFO] Task started: Blastn
[2023-03-15 16:22:13,364] [INFO] Running command: blastn -query OceanDNA-b23327/markers.fasta -db /var/lib/cwl/stg9f84e523-6678-4719-9eb7-847d0bd475e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:22:14,664] [INFO] Task succeeded: Blastn
[2023-03-15 16:22:14,669] [INFO] Selected 21 target genomes.
[2023-03-15 16:22:14,669] [INFO] Target genome list was writen to OceanDNA-b23327/target_genomes_gtdb.txt
[2023-03-15 16:22:14,834] [INFO] Task started: fastANI
[2023-03-15 16:22:14,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg467bf132-87ee-4253-bee7-5239b5ff1d16/OceanDNA-b23327.fa --refList OceanDNA-b23327/target_genomes_gtdb.txt --output OceanDNA-b23327/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:22:25,740] [INFO] Task succeeded: fastANI
[2023-03-15 16:22:25,753] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:22:25,753] [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_000466985.1	s__Brevundimonas abyssalis	89.0587	120	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_013823285.1	s__Brevundimonas sp013823285	87.821	123	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003938605.1	s__Brevundimonas sp003938605	80.115	88	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCA_017308115.1	s__Brevundimonas sp017308115	79.8884	88	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430835.1	s__Brevundimonas sp002430835	79.8704	83	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
GCA_002386585.1	s__Brevundimonas sp002386585	79.7601	70	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCF_000204035.1	s__Brevundimonas diminuta	79.7554	91	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCA_001794825.1	s__Brevundimonas sp001794825	79.7153	89	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	79.7034	88	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	79.6524	87	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427825.1	s__Brevundimonas sp001427825	79.6112	82	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	79.4093	92	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	79.3953	90	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	79.3439	78	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	79.2737	77	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934285.1	s__Brevundimonas fluminis	79.185	86	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003704105.1	s__Brevundimonas lutea	78.9353	93	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	78.6671	67	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	77.8094	56	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_016125585.1	s__Caulobacter sp016125585	77.6338	52	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241625.1	s__Phenylobacterium sp018241625	76.4208	51	140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:22:25,758] [INFO] GTDB search result was written to OceanDNA-b23327/result_gtdb.tsv
[2023-03-15 16:22:25,763] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:22:25,770] [INFO] DFAST_QC result json was written to OceanDNA-b23327/dqc_result.json
[2023-03-15 16:22:25,770] [INFO] DFAST_QC completed!
[2023-03-15 16:22:25,770] [INFO] Total running time: 0h0m52s