[2024-01-25 18:49:05,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:05,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:05,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference
[2024-01-25 18:49:06,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:06,962] [INFO] Task started: Prodigal
[2024-01-25 18:49:06,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg156edc7f-ab21-48cd-b68e-e31c6b487c59/GCF_000466985.1_ASM46698v1_genomic.fna.gz | prodigal -d GCF_000466985.1_ASM46698v1_genomic.fna/cds.fna -a GCF_000466985.1_ASM46698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:14,027] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:14,027] [INFO] Task started: HMMsearch
[2024-01-25 18:49:14,027] [INFO] Running command: hmmsearch --tblout GCF_000466985.1_ASM46698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/reference_markers.hmm GCF_000466985.1_ASM46698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:14,232] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:14,233] [INFO] Found 6/6 markers.
[2024-01-25 18:49:14,260] [INFO] Query marker FASTA was written to GCF_000466985.1_ASM46698v1_genomic.fna/markers.fasta
[2024-01-25 18:49:14,260] [INFO] Task started: Blastn
[2024-01-25 18:49:14,260] [INFO] Running command: blastn -query GCF_000466985.1_ASM46698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/reference_markers.fasta -out GCF_000466985.1_ASM46698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:15,204] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:15,207] [INFO] Selected 20 target genomes.
[2024-01-25 18:49:15,207] [INFO] Target genome list was writen to GCF_000466985.1_ASM46698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:15,220] [INFO] Task started: fastANI
[2024-01-25 18:49:15,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg156edc7f-ab21-48cd-b68e-e31c6b487c59/GCF_000466985.1_ASM46698v1_genomic.fna.gz --refList GCF_000466985.1_ASM46698v1_genomic.fna/target_genomes.txt --output GCF_000466985.1_ASM46698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:27,833] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:27,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:27,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:27,845] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:49:27,845] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:49:27,846] [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 albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.1131	524	935	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.8492	491	935	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.7794	498	935	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.7412	508	935	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.7206	503	935	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.7072	488	935	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.5939	512	935	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.5848	461	935	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	80.5819	483	935	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.5639	529	935	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.4455	471	935	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.437	488	935	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.4264	506	935	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	80.3566	444	935	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	80.3328	486	935	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	80.3095	446	935	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.079	480	935	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.5336	435	935	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.518	403	935	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.092	280	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:27,847] [INFO] DFAST Taxonomy check result was written to GCF_000466985.1_ASM46698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:27,848] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:27,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:27,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/checkm_data
[2024-01-25 18:49:27,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:27,879] [INFO] Task started: CheckM
[2024-01-25 18:49:27,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000466985.1_ASM46698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000466985.1_ASM46698v1_genomic.fna/checkm_input GCF_000466985.1_ASM46698v1_genomic.fna/checkm_result
[2024-01-25 18:49:54,503] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:54,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:54,524] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:54,525] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:54,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000466985.1_ASM46698v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:54,525] [INFO] Task started: Blastn
[2024-01-25 18:49:54,525] [INFO] Running command: blastn -query GCF_000466985.1_ASM46698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f2f37bf-6328-40ed-9e86-02efcb549439/dqc_reference/reference_markers_gtdb.fasta -out GCF_000466985.1_ASM46698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:56,421] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:56,425] [INFO] Selected 19 target genomes.
[2024-01-25 18:49:56,425] [INFO] Target genome list was writen to GCF_000466985.1_ASM46698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:56,441] [INFO] Task started: fastANI
[2024-01-25 18:49:56,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg156edc7f-ab21-48cd-b68e-e31c6b487c59/GCF_000466985.1_ASM46698v1_genomic.fna.gz --refList GCF_000466985.1_ASM46698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000466985.1_ASM46698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:09,218] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:09,230] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:09,230] [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_000466985.1	s__Brevundimonas abyssalis	100.0	930	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	conclusive
GCA_013823285.1	s__Brevundimonas sp013823285	92.6184	667	935	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	81.1201	493	935	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	81.0378	510	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003938605.1	s__Brevundimonas sp003938605	80.9527	507	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCA_017308115.1	s__Brevundimonas sp017308115	80.9488	477	935	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	80.8821	457	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016183935.1	s__Brevundimonas sp016183935	80.8032	468	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	80.7986	508	935	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	80.745	506	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_000204035.1	s__Brevundimonas diminuta	80.7264	501	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCF_000421705.1	s__Brevundimonas naejangsanensis	80.7074	488	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.43	97.43	0.89	0.89	2	-
GCA_002386585.1	s__Brevundimonas sp002386585	80.6991	426	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCF_001424025.1	s__Brevundimonas sp001424025	80.6306	488	935	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	80.6278	432	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836405.1	s__Brevundimonas sp014836405	80.6189	458	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730275.1	s__Brevundimonas halotolerans	80.3347	444	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCA_016742135.1	s__Brevundimonas sp016742135	80.3196	429	935	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	80.1945	469	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:09,231] [INFO] GTDB search result was written to GCF_000466985.1_ASM46698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:09,232] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:09,235] [INFO] DFAST_QC result json was written to GCF_000466985.1_ASM46698v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:09,236] [INFO] DFAST_QC completed!
[2024-01-25 18:50:09,236] [INFO] Total running time: 0h1m3s