[2023-03-19 02:46:09,190] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:46:09,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:46:09,190] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference
[2023-03-19 02:46:10,278] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:46:10,279] [INFO] Task started: Prodigal
[2023-03-19 02:46:10,279] [INFO] Running command: cat /var/lib/cwl/stgde088c3a-8849-45df-912f-6461940b3e18/OceanDNA-b23331.fa | prodigal -d OceanDNA-b23331/cds.fna -a OceanDNA-b23331/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:46:20,479] [INFO] Task succeeded: Prodigal
[2023-03-19 02:46:20,479] [INFO] Task started: HMMsearch
[2023-03-19 02:46:20,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b23331/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/reference_markers.hmm OceanDNA-b23331/protein.faa > /dev/null
[2023-03-19 02:46:20,647] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:46:20,647] [INFO] Found 6/6 markers.
[2023-03-19 02:46:20,665] [INFO] Query marker FASTA was written to OceanDNA-b23331/markers.fasta
[2023-03-19 02:46:20,666] [INFO] Task started: Blastn
[2023-03-19 02:46:20,666] [INFO] Running command: blastn -query OceanDNA-b23331/markers.fasta -db /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/reference_markers.fasta -out OceanDNA-b23331/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:46:21,431] [INFO] Task succeeded: Blastn
[2023-03-19 02:46:21,433] [INFO] Selected 17 target genomes.
[2023-03-19 02:46:21,433] [INFO] Target genome list was writen to OceanDNA-b23331/target_genomes.txt
[2023-03-19 02:46:21,501] [INFO] Task started: fastANI
[2023-03-19 02:46:21,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgde088c3a-8849-45df-912f-6461940b3e18/OceanDNA-b23331.fa --refList OceanDNA-b23331/target_genomes.txt --output OceanDNA-b23331/fastani_result.tsv --threads 1
[2023-03-19 02:46:31,310] [INFO] Task succeeded: fastANI
[2023-03-19 02:46:31,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:46:31,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:46:31,321] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:46:31,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:46:31,321] [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=MCS24	GCA_003730275.1	69670	69670	type	True	89.8458	512	561	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	89.841	512	561	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.6735	359	561	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.3717	360	561	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.2497	342	561	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.2044	352	561	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.1574	360	561	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.1074	323	561	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.0855	336	561	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.0334	350	561	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	79.9846	361	561	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	79.9777	340	561	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.9329	373	561	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	79.8555	351	561	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	79.7826	312	561	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.5878	192	561	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.2972	174	561	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:46:31,322] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23331/tc_result.tsv
[2023-03-19 02:46:31,325] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:46:31,325] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:46:31,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/checkm_data
[2023-03-19 02:46:31,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:46:31,330] [INFO] Task started: CheckM
[2023-03-19 02:46:31,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23331/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23331/checkm_input OceanDNA-b23331/checkm_result
[2023-03-19 02:47:01,667] [INFO] Task succeeded: CheckM
[2023-03-19 02:47:01,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:47:01,671] [INFO] ===== Completeness check finished =====
[2023-03-19 02:47:01,671] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:47:01,671] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23331/markers.fasta)
[2023-03-19 02:47:01,672] [INFO] Task started: Blastn
[2023-03-19 02:47:01,672] [INFO] Running command: blastn -query OceanDNA-b23331/markers.fasta -db /var/lib/cwl/stgdcc8ae28-fbca-41e0-93d8-1098815d810d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23331/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:47:03,379] [INFO] Task succeeded: Blastn
[2023-03-19 02:47:03,381] [INFO] Selected 13 target genomes.
[2023-03-19 02:47:03,381] [INFO] Target genome list was writen to OceanDNA-b23331/target_genomes_gtdb.txt
[2023-03-19 02:47:03,455] [INFO] Task started: fastANI
[2023-03-19 02:47:03,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgde088c3a-8849-45df-912f-6461940b3e18/OceanDNA-b23331.fa --refList OceanDNA-b23331/target_genomes_gtdb.txt --output OceanDNA-b23331/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:47:10,769] [INFO] Task succeeded: fastANI
[2023-03-19 02:47:10,777] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:47:10,777] [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	89.8458	512	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCA_018826885.1	s__Brevundimonas sp018826885	88.65	444	561	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	88.021	500	561	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	87.9405	502	561	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	80.5915	349	561	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	80.5064	383	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_002002865.1	s__Brevundimonas sp002002865	80.225	330	561	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	80.2148	328	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302335.1	s__Brevundimonas sp017302335	80.1997	312	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	80.1576	360	561	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	80.0606	354	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683885.1	s__Brevundimonas sp004683885	80.0464	309	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000466985.1	s__Brevundimonas abyssalis	79.7296	305	561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:47:10,778] [INFO] GTDB search result was written to OceanDNA-b23331/result_gtdb.tsv
[2023-03-19 02:47:10,779] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:47:10,781] [INFO] DFAST_QC result json was written to OceanDNA-b23331/dqc_result.json
[2023-03-19 02:47:10,781] [INFO] DFAST_QC completed!
[2023-03-19 02:47:10,781] [INFO] Total running time: 0h1m2s