[2023-06-13 18:12:32,848] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:12:32,849] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:12:32,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference
[2023-06-13 18:12:34,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:12:34,410] [INFO] Task started: Prodigal
[2023-06-13 18:12:34,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg23f04cd2-47fb-4758-8195-c82646dab25a/GCA_947484875.1_TE-Jun18-248_genomic.fna.gz | prodigal -d GCA_947484875.1_TE-Jun18-248_genomic.fna/cds.fna -a GCA_947484875.1_TE-Jun18-248_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:12:38,752] [INFO] Task succeeded: Prodigal
[2023-06-13 18:12:38,752] [INFO] Task started: HMMsearch
[2023-06-13 18:12:38,752] [INFO] Running command: hmmsearch --tblout GCA_947484875.1_TE-Jun18-248_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/reference_markers.hmm GCA_947484875.1_TE-Jun18-248_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:12:38,957] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:12:38,958] [INFO] Found 6/6 markers.
[2023-06-13 18:12:38,983] [INFO] Query marker FASTA was written to GCA_947484875.1_TE-Jun18-248_genomic.fna/markers.fasta
[2023-06-13 18:12:38,984] [INFO] Task started: Blastn
[2023-06-13 18:12:38,984] [INFO] Running command: blastn -query GCA_947484875.1_TE-Jun18-248_genomic.fna/markers.fasta -db /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/reference_markers.fasta -out GCA_947484875.1_TE-Jun18-248_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:12:39,838] [INFO] Task succeeded: Blastn
[2023-06-13 18:12:39,844] [INFO] Selected 15 target genomes.
[2023-06-13 18:12:39,844] [INFO] Target genome list was writen to GCA_947484875.1_TE-Jun18-248_genomic.fna/target_genomes.txt
[2023-06-13 18:12:39,845] [INFO] Task started: fastANI
[2023-06-13 18:12:39,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f04cd2-47fb-4758-8195-c82646dab25a/GCA_947484875.1_TE-Jun18-248_genomic.fna.gz --refList GCA_947484875.1_TE-Jun18-248_genomic.fna/target_genomes.txt --output GCA_947484875.1_TE-Jun18-248_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:12:49,028] [INFO] Task succeeded: fastANI
[2023-06-13 18:12:49,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:12:49,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:12:49,039] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:12:49,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:12:49,039] [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 basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	83.3293	403	583	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	83.2094	434	583	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	82.8328	441	583	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	82.0616	425	583	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.283	397	583	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.2088	389	583	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.7386	373	583	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.7065	361	583	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.7007	355	583	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.3907	353	583	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.366	339	583	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.2813	360	583	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.135	333	583	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.4117	216	583	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.9065	224	583	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:12:49,041] [INFO] DFAST Taxonomy check result was written to GCA_947484875.1_TE-Jun18-248_genomic.fna/tc_result.tsv
[2023-06-13 18:12:49,042] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:12:49,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:12:49,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/checkm_data
[2023-06-13 18:12:49,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:12:49,067] [INFO] Task started: CheckM
[2023-06-13 18:12:49,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947484875.1_TE-Jun18-248_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947484875.1_TE-Jun18-248_genomic.fna/checkm_input GCA_947484875.1_TE-Jun18-248_genomic.fna/checkm_result
[2023-06-13 18:13:07,184] [INFO] Task succeeded: CheckM
[2023-06-13 18:13:07,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.18%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:13:07,222] [INFO] ===== Completeness check finished =====
[2023-06-13 18:13:07,223] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:13:07,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947484875.1_TE-Jun18-248_genomic.fna/markers.fasta)
[2023-06-13 18:13:07,224] [INFO] Task started: Blastn
[2023-06-13 18:13:07,224] [INFO] Running command: blastn -query GCA_947484875.1_TE-Jun18-248_genomic.fna/markers.fasta -db /var/lib/cwl/stg52184cbb-fd09-435a-a417-35c8fb14ca01/dqc_reference/reference_markers_gtdb.fasta -out GCA_947484875.1_TE-Jun18-248_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:13:08,816] [INFO] Task succeeded: Blastn
[2023-06-13 18:13:08,820] [INFO] Selected 11 target genomes.
[2023-06-13 18:13:08,820] [INFO] Target genome list was writen to GCA_947484875.1_TE-Jun18-248_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:13:08,846] [INFO] Task started: fastANI
[2023-06-13 18:13:08,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f04cd2-47fb-4758-8195-c82646dab25a/GCA_947484875.1_TE-Jun18-248_genomic.fna.gz --refList GCA_947484875.1_TE-Jun18-248_genomic.fna/target_genomes_gtdb.txt --output GCA_947484875.1_TE-Jun18-248_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:13:15,205] [INFO] Task succeeded: fastANI
[2023-06-13 18:13:15,212] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:13:15,213] [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_002483305.1	s__Brevundimonas sp002483305	86.4729	444	583	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	86.386	463	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_004296955.1	s__Brevundimonas sp004296955	86.3732	466	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_002343425.1	s__Brevundimonas sp002343425	86.2621	461	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.78	0.93	0.93	2	-
GCA_006515835.1	s__Brevundimonas sp006515835	86.2407	403	583	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	85.1253	453	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	83.315	405	583	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	83.2095	434	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820665.1	s__Brevundimonas sp018820665	83.1284	389	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_001425945.1	s__Brevundimonas sp001425945	82.6362	429	583	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	82.1917	421	583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:13:15,214] [INFO] GTDB search result was written to GCA_947484875.1_TE-Jun18-248_genomic.fna/result_gtdb.tsv
[2023-06-13 18:13:15,215] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:13:15,218] [INFO] DFAST_QC result json was written to GCA_947484875.1_TE-Jun18-248_genomic.fna/dqc_result.json
[2023-06-13 18:13:15,218] [INFO] DFAST_QC completed!
[2023-06-13 18:13:15,218] [INFO] Total running time: 0h0m42s