[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,930] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,931] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f86f97-bf18-4099-8a06-1e1b96088c8c/GCF_016656965.1_ASM1665696v1_genomic.fna.gz | prodigal -d GCF_016656965.1_ASM1665696v1_genomic.fna/cds.fna -a GCF_016656965.1_ASM1665696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,327] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,328] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,328] [INFO] Running command: hmmsearch --tblout GCF_016656965.1_ASM1665696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/reference_markers.hmm GCF_016656965.1_ASM1665696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,635] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,665] [INFO] Query marker FASTA was written to GCF_016656965.1_ASM1665696v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,665] [INFO] Task started: Blastn
[2024-01-24 10:47:20,666] [INFO] Running command: blastn -query GCF_016656965.1_ASM1665696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/reference_markers.fasta -out GCF_016656965.1_ASM1665696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,486] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,491] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:21,492] [INFO] Target genome list was writen to GCF_016656965.1_ASM1665696v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,840] [INFO] Task started: fastANI
[2024-01-24 10:47:23,841] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f86f97-bf18-4099-8a06-1e1b96088c8c/GCF_016656965.1_ASM1665696v1_genomic.fna.gz --refList GCF_016656965.1_ASM1665696v1_genomic.fna/target_genomes.txt --output GCF_016656965.1_ASM1665696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:39,535] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:39,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:39,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:39,558] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:39,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:39,559] [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 vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	100.0	992	992	95	conclusive
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.1594	586	992	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.0593	554	992	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.6826	538	992	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.5618	585	992	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.5518	523	992	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.4905	545	992	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.4332	561	992	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	80.4314	533	992	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.4272	562	992	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.4114	514	992	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.3565	515	992	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.2805	549	992	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.229	541	992	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.1674	527	992	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.1112	500	992	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.0819	491	992	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	79.9921	514	992	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.196	336	992	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	76.9891	80	992	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.3115	141	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:39,561] [INFO] DFAST Taxonomy check result was written to GCF_016656965.1_ASM1665696v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:39,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:39,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:39,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/checkm_data
[2024-01-24 10:47:39,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:39,599] [INFO] Task started: CheckM
[2024-01-24 10:47:39,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016656965.1_ASM1665696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016656965.1_ASM1665696v1_genomic.fna/checkm_input GCF_016656965.1_ASM1665696v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,771] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,799] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016656965.1_ASM1665696v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,801] [INFO] Task started: Blastn
[2024-01-24 10:48:09,801] [INFO] Running command: blastn -query GCF_016656965.1_ASM1665696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b79d269-a825-4c49-8f67-c5ac855a234d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016656965.1_ASM1665696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,310] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,314] [INFO] Selected 24 target genomes.
[2024-01-24 10:48:11,314] [INFO] Target genome list was writen to GCF_016656965.1_ASM1665696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:11,429] [INFO] Task started: fastANI
[2024-01-24 10:48:11,430] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f86f97-bf18-4099-8a06-1e1b96088c8c/GCF_016656965.1_ASM1665696v1_genomic.fna.gz --refList GCF_016656965.1_ASM1665696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016656965.1_ASM1665696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:27,840] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,861] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:27,861] [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_016656965.1	s__Brevundimonas sp016656965	100.0	991	992	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_002002865.1	s__Brevundimonas sp002002865	81.1856	592	992	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	81.1747	549	992	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	81.1676	585	992	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	80.856	533	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCF_002157625.1	s__Brevundimonas sp002157625	80.8542	556	992	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	80.7517	558	992	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	80.7455	544	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_016463295.1	s__Brevundimonas sp016463295	80.6592	530	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434505.1	s__Brevundimonas sp002434505	80.6183	569	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCA_003248965.1	s__Brevundimonas sp003248965	80.5613	538	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.48	95.48	0.80	0.80	2	-
GCF_017487405.1	s__Brevundimonas sp017487405	80.5517	589	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701445.1	s__Brevundimonas bacteroides	80.5316	526	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295975.1	s__Brevundimonas sp001295975	80.4478	482	992	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	80.446	531	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
GCF_004683885.1	s__Brevundimonas sp004683885	80.4456	491	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014196335.1	s__Brevundimonas lenta	80.4275	562	992	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	80.4	515	992	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	80.3518	499	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479325.1	s__Brevundimonas sp002479325	80.2348	485	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547065.1	s__Brevundimonas sp006547065	80.1047	562	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292165.1	s__Brevundimonas sp002292165	80.096	492	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890385.1	s__Tardibacter chloracetimidivorans	76.8611	79	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,863] [INFO] GTDB search result was written to GCF_016656965.1_ASM1665696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:27,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:27,868] [INFO] DFAST_QC result json was written to GCF_016656965.1_ASM1665696v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:27,869] [INFO] DFAST_QC completed!
[2024-01-24 10:48:27,869] [INFO] Total running time: 0h1m21s