[2023-03-16 18:07:32,435] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:32,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:32,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference
[2023-03-16 18:07:34,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:34,761] [INFO] Task started: Prodigal
[2023-03-16 18:07:34,762] [INFO] Running command: cat /var/lib/cwl/stg009db3d8-90b9-4f0e-89b5-a1502a528849/OceanDNA-b23415.fa | prodigal -d OceanDNA-b23415/cds.fna -a OceanDNA-b23415/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:49,711] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:49,711] [INFO] Task started: HMMsearch
[2023-03-16 18:07:49,712] [INFO] Running command: hmmsearch --tblout OceanDNA-b23415/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/reference_markers.hmm OceanDNA-b23415/protein.faa > /dev/null
[2023-03-16 18:07:49,873] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:49,873] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg009db3d8-90b9-4f0e-89b5-a1502a528849/OceanDNA-b23415.fa]
[2023-03-16 18:07:49,893] [INFO] Query marker FASTA was written to OceanDNA-b23415/markers.fasta
[2023-03-16 18:07:49,894] [INFO] Task started: Blastn
[2023-03-16 18:07:49,894] [INFO] Running command: blastn -query OceanDNA-b23415/markers.fasta -db /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/reference_markers.fasta -out OceanDNA-b23415/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:50,522] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:50,523] [INFO] Selected 13 target genomes.
[2023-03-16 18:07:50,523] [INFO] Target genome list was writen to OceanDNA-b23415/target_genomes.txt
[2023-03-16 18:07:50,553] [INFO] Task started: fastANI
[2023-03-16 18:07:50,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg009db3d8-90b9-4f0e-89b5-a1502a528849/OceanDNA-b23415.fa --refList OceanDNA-b23415/target_genomes.txt --output OceanDNA-b23415/fastani_result.tsv --threads 1
[2023-03-16 18:07:59,130] [INFO] Task succeeded: fastANI
[2023-03-16 18:07:59,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:07:59,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:07:59,139] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 18:07:59,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 18:07:59,139] [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 aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	97.2356	595	640	95	conclusive
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	87.4978	527	640	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	84.9056	504	640	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	84.8918	496	640	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.3842	486	640	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	83.6794	470	640	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	81.5286	419	640	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	81.5089	419	640	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.2927	385	640	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.0541	334	640	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	79.937	342	640	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.2737	229	640	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.8446	234	640	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:07:59,140] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23415/tc_result.tsv
[2023-03-16 18:07:59,140] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:07:59,140] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:07:59,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/checkm_data
[2023-03-16 18:07:59,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:07:59,145] [INFO] Task started: CheckM
[2023-03-16 18:07:59,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23415/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23415/checkm_input OceanDNA-b23415/checkm_result
[2023-03-16 18:08:30,873] [INFO] Task succeeded: CheckM
[2023-03-16 18:08:30,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:08:30,876] [INFO] ===== Completeness check finished =====
[2023-03-16 18:08:30,876] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:08:30,876] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23415/markers.fasta)
[2023-03-16 18:08:30,877] [INFO] Task started: Blastn
[2023-03-16 18:08:30,877] [INFO] Running command: blastn -query OceanDNA-b23415/markers.fasta -db /var/lib/cwl/stgdb7afdd4-e253-4ba9-931a-e98e460375d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23415/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:08:31,918] [INFO] Task succeeded: Blastn
[2023-03-16 18:08:31,919] [INFO] Selected 11 target genomes.
[2023-03-16 18:08:31,919] [INFO] Target genome list was writen to OceanDNA-b23415/target_genomes_gtdb.txt
[2023-03-16 18:08:31,930] [INFO] Task started: fastANI
[2023-03-16 18:08:31,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg009db3d8-90b9-4f0e-89b5-a1502a528849/OceanDNA-b23415.fa --refList OceanDNA-b23415/target_genomes_gtdb.txt --output OceanDNA-b23415/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:08:39,359] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:39,366] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:08:39,366] [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_014199955.1	s__Brevundimonas aurantiaca	97.2356	595	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.57	96.95	0.92	0.85	12	conclusive
GCA_001796045.1	s__Brevundimonas sp001796045	88.3897	467	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	87.6154	534	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_014196125.1	s__Brevundimonas mediterranea	87.4978	527	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	86.8595	530	640	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	85.3389	517	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506205.1	s__Brevundimonas sp902506205	85.1864	501	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248455.1	s__Brevundimonas sp003248455	84.9711	476	640	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	81.8119	386	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210735.1	s__Brevundimonas sp004210735	81.5032	381	640	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	81.4709	371	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:08:39,367] [INFO] GTDB search result was written to OceanDNA-b23415/result_gtdb.tsv
[2023-03-16 18:08:39,368] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:08:39,370] [INFO] DFAST_QC result json was written to OceanDNA-b23415/dqc_result.json
[2023-03-16 18:08:39,370] [INFO] DFAST_QC completed!
[2023-03-16 18:08:39,370] [INFO] Total running time: 0h1m7s