[2023-03-16 21:13:50,934] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:13:50,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:13:50,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference
[2023-03-16 21:13:53,145] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:13:53,145] [INFO] Task started: Prodigal
[2023-03-16 21:13:53,145] [INFO] Running command: cat /var/lib/cwl/stgb17c3aa7-a8d5-4c15-bbff-e133ae50e8b6/OceanDNA-b23399.fa | prodigal -d OceanDNA-b23399/cds.fna -a OceanDNA-b23399/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:14:11,899] [INFO] Task succeeded: Prodigal
[2023-03-16 21:14:11,899] [INFO] Task started: HMMsearch
[2023-03-16 21:14:11,899] [INFO] Running command: hmmsearch --tblout OceanDNA-b23399/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/reference_markers.hmm OceanDNA-b23399/protein.faa > /dev/null
[2023-03-16 21:14:12,090] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:14:12,090] [INFO] Found 6/6 markers.
[2023-03-16 21:14:12,108] [INFO] Query marker FASTA was written to OceanDNA-b23399/markers.fasta
[2023-03-16 21:14:12,109] [INFO] Task started: Blastn
[2023-03-16 21:14:12,109] [INFO] Running command: blastn -query OceanDNA-b23399/markers.fasta -db /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/reference_markers.fasta -out OceanDNA-b23399/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:14:12,927] [INFO] Task succeeded: Blastn
[2023-03-16 21:14:12,928] [INFO] Selected 14 target genomes.
[2023-03-16 21:14:12,928] [INFO] Target genome list was writen to OceanDNA-b23399/target_genomes.txt
[2023-03-16 21:14:12,937] [INFO] Task started: fastANI
[2023-03-16 21:14:12,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17c3aa7-a8d5-4c15-bbff-e133ae50e8b6/OceanDNA-b23399.fa --refList OceanDNA-b23399/target_genomes.txt --output OceanDNA-b23399/fastani_result.tsv --threads 1
[2023-03-16 21:14:22,431] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:22,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:14:22,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:14:22,440] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:14:22,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:14:22,440] [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 alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.7239	587	993	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.5791	612	993	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.4547	569	993	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.3362	583	993	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.0522	546	993	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.7846	539	993	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	80.7773	539	993	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.7656	597	993	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.7604	506	993	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.7439	558	993	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.6991	546	993	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.2944	502	993	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.1624	319	993	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.0729	71	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:14:22,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23399/tc_result.tsv
[2023-03-16 21:14:22,440] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:14:22,440] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:14:22,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/checkm_data
[2023-03-16 21:14:22,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:14:22,446] [INFO] Task started: CheckM
[2023-03-16 21:14:22,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23399/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23399/checkm_input OceanDNA-b23399/checkm_result
[2023-03-16 21:15:12,269] [INFO] Task succeeded: CheckM
[2023-03-16 21:15:12,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 1.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 21:15:12,272] [INFO] ===== Completeness check finished =====
[2023-03-16 21:15:12,272] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:15:12,272] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23399/markers.fasta)
[2023-03-16 21:15:12,273] [INFO] Task started: Blastn
[2023-03-16 21:15:12,273] [INFO] Running command: blastn -query OceanDNA-b23399/markers.fasta -db /var/lib/cwl/stg811cc4d1-e643-4fb6-bdb1-5cf4f8d38901/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23399/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:15:13,917] [INFO] Task succeeded: Blastn
[2023-03-16 21:15:13,918] [INFO] Selected 18 target genomes.
[2023-03-16 21:15:13,918] [INFO] Target genome list was writen to OceanDNA-b23399/target_genomes_gtdb.txt
[2023-03-16 21:15:14,014] [INFO] Task started: fastANI
[2023-03-16 21:15:14,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgb17c3aa7-a8d5-4c15-bbff-e133ae50e8b6/OceanDNA-b23399.fa --refList OceanDNA-b23399/target_genomes_gtdb.txt --output OceanDNA-b23399/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:15:33,544] [INFO] Task succeeded: fastANI
[2023-03-16 21:15:33,554] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:15:33,554] [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_016463295.1	s__Brevundimonas sp016463295	89.4719	667	993	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	82.6644	585	993	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	82.5257	613	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	82.3065	602	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_018826515.1	s__Brevundimonas sp018826515	82.3006	614	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_016183935.1	s__Brevundimonas sp016183935	81.9931	556	993	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	81.7154	589	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006515835.1	s__Brevundimonas sp006515835	81.6939	489	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343425.1	s__Brevundimonas sp002343425	81.6934	541	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.78	0.93	0.93	2	-
GCA_016742215.1	s__Brevundimonas sp016742215	81.5257	412	993	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	81.4546	569	993	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	81.3256	571	993	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	81.2032	375	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614235.1	s__Brevundimonas intermedia	81.0111	557	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	80.7936	554	993	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	80.7553	557	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280475.1	s__Brevundimonas subvibrioides_C	80.6984	535	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
GCF_014199945.1	s__Brevundimonas variabilis	80.2916	502	993	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 21:15:33,554] [INFO] GTDB search result was written to OceanDNA-b23399/result_gtdb.tsv
[2023-03-16 21:15:33,554] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:15:33,556] [INFO] DFAST_QC result json was written to OceanDNA-b23399/dqc_result.json
[2023-03-16 21:15:33,556] [INFO] DFAST_QC completed!
[2023-03-16 21:15:33,556] [INFO] Total running time: 0h1m43s