[2023-03-16 07:13:34,679] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:13:34,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:13:34,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference
[2023-03-16 07:13:35,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:13:35,854] [INFO] Task started: Prodigal
[2023-03-16 07:13:35,854] [INFO] Running command: cat /var/lib/cwl/stgc4fd9deb-e1cf-4398-bcc0-215f322336c3/OceanDNA-b23417.fa | prodigal -d OceanDNA-b23417/cds.fna -a OceanDNA-b23417/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:13:56,646] [INFO] Task succeeded: Prodigal
[2023-03-16 07:13:56,646] [INFO] Task started: HMMsearch
[2023-03-16 07:13:56,646] [INFO] Running command: hmmsearch --tblout OceanDNA-b23417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/reference_markers.hmm OceanDNA-b23417/protein.faa > /dev/null
[2023-03-16 07:13:56,846] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:13:56,847] [INFO] Found 6/6 markers.
[2023-03-16 07:13:56,869] [INFO] Query marker FASTA was written to OceanDNA-b23417/markers.fasta
[2023-03-16 07:13:56,871] [INFO] Task started: Blastn
[2023-03-16 07:13:56,871] [INFO] Running command: blastn -query OceanDNA-b23417/markers.fasta -db /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/reference_markers.fasta -out OceanDNA-b23417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:13:57,702] [INFO] Task succeeded: Blastn
[2023-03-16 07:13:57,703] [INFO] Selected 19 target genomes.
[2023-03-16 07:13:57,703] [INFO] Target genome list was writen to OceanDNA-b23417/target_genomes.txt
[2023-03-16 07:13:57,715] [INFO] Task started: fastANI
[2023-03-16 07:13:57,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fd9deb-e1cf-4398-bcc0-215f322336c3/OceanDNA-b23417.fa --refList OceanDNA-b23417/target_genomes.txt --output OceanDNA-b23417/fastani_result.tsv --threads 1
[2023-03-16 07:14:11,638] [INFO] Task succeeded: fastANI
[2023-03-16 07:14:11,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:14:11,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:14:11,649] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:14:11,649] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:14:11,650] [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 goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	91.0324	963	1193	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	82.3363	660	1193	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.1489	615	1193	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	82.0138	635	1193	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.9439	662	1193	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	81.8912	638	1193	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	81.8408	631	1193	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	81.7703	582	1193	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.7398	614	1193	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	81.696	590	1193	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.6486	550	1193	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	81.502	584	1193	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.4921	550	1193	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.4268	623	1193	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5517	541	1193	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.2867	526	1193	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.7805	334	1193	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.5949	478	1193	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.2385	396	1193	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:14:11,650] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23417/tc_result.tsv
[2023-03-16 07:14:11,650] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:14:11,650] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:14:11,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/checkm_data
[2023-03-16 07:14:11,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:14:11,656] [INFO] Task started: CheckM
[2023-03-16 07:14:11,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23417/checkm_input OceanDNA-b23417/checkm_result
[2023-03-16 07:15:03,763] [INFO] Task succeeded: CheckM
[2023-03-16 07:15:03,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:15:03,766] [INFO] ===== Completeness check finished =====
[2023-03-16 07:15:03,766] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:15:03,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23417/markers.fasta)
[2023-03-16 07:15:03,768] [INFO] Task started: Blastn
[2023-03-16 07:15:03,768] [INFO] Running command: blastn -query OceanDNA-b23417/markers.fasta -db /var/lib/cwl/stg9599db51-cd1d-4f00-828a-526b08390620/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:15:05,415] [INFO] Task succeeded: Blastn
[2023-03-16 07:15:05,416] [INFO] Selected 18 target genomes.
[2023-03-16 07:15:05,416] [INFO] Target genome list was writen to OceanDNA-b23417/target_genomes_gtdb.txt
[2023-03-16 07:15:05,427] [INFO] Task started: fastANI
[2023-03-16 07:15:05,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fd9deb-e1cf-4398-bcc0-215f322336c3/OceanDNA-b23417.fa --refList OceanDNA-b23417/target_genomes_gtdb.txt --output OceanDNA-b23417/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:15:19,358] [INFO] Task succeeded: fastANI
[2023-03-16 07:15:19,369] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:15:19,370] [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_002292165.1	s__Brevundimonas sp002292165	99.6795	950	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017487405.1	s__Brevundimonas sp017487405	91.0495	962	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463485.1	s__Brevundimonas sp016463485	82.7403	649	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280785.1	s__Brevundimonas subvibrioides_B	82.6487	669	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144605.1	s__Brevundimonas subvibrioides	82.3247	661	1193	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	82.2782	633	1193	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	82.2485	566	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479495.1	s__Brevundimonas sp002479495	82.2232	610	1193	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	82.0258	602	1193	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	82.0235	611	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCF_014196335.1	s__Brevundimonas lenta	81.9643	660	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826515.1	s__Brevundimonas sp018826515	81.9499	584	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_003248455.1	s__Brevundimonas sp003248455	81.8677	593	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	81.84	604	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795885.1	s__Brevundimonas sp017795885	81.8134	604	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248925.1	s__Brevundimonas sp003248925	81.8076	516	1193	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	81.6529	597	1193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
GCF_000701445.1	s__Brevundimonas bacteroides	81.495	584	1193	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 07:15:19,370] [INFO] GTDB search result was written to OceanDNA-b23417/result_gtdb.tsv
[2023-03-16 07:15:19,370] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:15:19,373] [INFO] DFAST_QC result json was written to OceanDNA-b23417/dqc_result.json
[2023-03-16 07:15:19,373] [INFO] DFAST_QC completed!
[2023-03-16 07:15:19,373] [INFO] Total running time: 0h1m45s