[2023-03-16 09:26:56,821] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:26:56,821] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:26:56,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference
[2023-03-16 09:26:57,921] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:26:57,921] [INFO] Task started: Prodigal
[2023-03-16 09:26:57,921] [INFO] Running command: cat /var/lib/cwl/stg3e0a976a-c417-4ce7-bd1c-8e698870d622/OceanDNA-b23435.fa | prodigal -d OceanDNA-b23435/cds.fna -a OceanDNA-b23435/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:27:13,143] [INFO] Task succeeded: Prodigal
[2023-03-16 09:27:13,144] [INFO] Task started: HMMsearch
[2023-03-16 09:27:13,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b23435/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/reference_markers.hmm OceanDNA-b23435/protein.faa > /dev/null
[2023-03-16 09:27:13,316] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:27:13,316] [INFO] Found 6/6 markers.
[2023-03-16 09:27:13,346] [INFO] Query marker FASTA was written to OceanDNA-b23435/markers.fasta
[2023-03-16 09:27:13,348] [INFO] Task started: Blastn
[2023-03-16 09:27:13,348] [INFO] Running command: blastn -query OceanDNA-b23435/markers.fasta -db /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/reference_markers.fasta -out OceanDNA-b23435/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:27:14,173] [INFO] Task succeeded: Blastn
[2023-03-16 09:27:14,176] [INFO] Selected 18 target genomes.
[2023-03-16 09:27:14,176] [INFO] Target genome list was writen to OceanDNA-b23435/target_genomes.txt
[2023-03-16 09:27:14,221] [INFO] Task started: fastANI
[2023-03-16 09:27:14,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e0a976a-c417-4ce7-bd1c-8e698870d622/OceanDNA-b23435.fa --refList OceanDNA-b23435/target_genomes.txt --output OceanDNA-b23435/fastani_result.tsv --threads 1
[2023-03-16 09:27:25,815] [INFO] Task succeeded: fastANI
[2023-03-16 09:27:25,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:27:25,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:27:25,827] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 09:27:25,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:27:25,827] [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 halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	97.069	773	829	95	conclusive
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	97.058	777	829	95	conclusive
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.9589	541	829	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.9074	500	829	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.6901	533	829	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.5973	510	829	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.5872	481	829	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.4926	529	829	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.4185	517	829	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.4043	498	829	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.3794	463	829	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.3542	507	829	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.313	471	829	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.2961	486	829	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.2706	468	829	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.2174	550	829	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.641	260	829	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8185	109	829	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:27:25,827] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23435/tc_result.tsv
[2023-03-16 09:27:25,827] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:27:25,827] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:27:25,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/checkm_data
[2023-03-16 09:27:25,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:27:25,836] [INFO] Task started: CheckM
[2023-03-16 09:27:25,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23435/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23435/checkm_input OceanDNA-b23435/checkm_result
[2023-03-16 09:28:05,936] [INFO] Task succeeded: CheckM
[2023-03-16 09:28:05,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:28:05,940] [INFO] ===== Completeness check finished =====
[2023-03-16 09:28:05,940] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:28:05,940] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23435/markers.fasta)
[2023-03-16 09:28:05,940] [INFO] Task started: Blastn
[2023-03-16 09:28:05,940] [INFO] Running command: blastn -query OceanDNA-b23435/markers.fasta -db /var/lib/cwl/stg3d9beed8-54d8-48d6-8308-1a5d6e868501/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23435/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:28:07,555] [INFO] Task succeeded: Blastn
[2023-03-16 09:28:07,557] [INFO] Selected 14 target genomes.
[2023-03-16 09:28:07,557] [INFO] Target genome list was writen to OceanDNA-b23435/target_genomes_gtdb.txt
[2023-03-16 09:28:07,572] [INFO] Task started: fastANI
[2023-03-16 09:28:07,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e0a976a-c417-4ce7-bd1c-8e698870d622/OceanDNA-b23435.fa --refList OceanDNA-b23435/target_genomes_gtdb.txt --output OceanDNA-b23435/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:28:16,594] [INFO] Task succeeded: fastANI
[2023-03-16 09:28:16,603] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:28:16,603] [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_003730275.1	s__Brevundimonas halotolerans	97.058	777	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	conclusive
GCA_018826885.1	s__Brevundimonas sp018826885	91.3315	602	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742135.1	s__Brevundimonas sp016742135	88.8773	724	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	86.7809	698	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820275.1	s__Brevundimonas sp018820275	81.1015	544	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_016183935.1	s__Brevundimonas sp016183935	81.0869	496	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202075.1	s__Brevundimonas basaltis	80.9424	542	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	80.8984	488	829	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	80.7648	496	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157625.1	s__Brevundimonas sp002157625	80.5258	502	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308115.1	s__Brevundimonas sp017308115	80.4979	461	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979535.1	s__Brevundimonas sp002979535	80.4388	505	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCF_017487345.1	s__Brevundimonas sp017487345	80.4068	518	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823285.1	s__Brevundimonas sp013823285	80.2012	431	829	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:28:16,605] [INFO] GTDB search result was written to OceanDNA-b23435/result_gtdb.tsv
[2023-03-16 09:28:16,609] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:28:16,614] [INFO] DFAST_QC result json was written to OceanDNA-b23435/dqc_result.json
[2023-03-16 09:28:16,614] [INFO] DFAST_QC completed!
[2023-03-16 09:28:16,614] [INFO] Total running time: 0h1m20s