[2024-01-24 11:20:34,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,065] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,065] [INFO] DQC Reference Directory: /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference
[2024-01-24 11:20:35,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,288] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,288] [INFO] Running command: gunzip -c /var/lib/cwl/stga95bc51b-a8e7-4065-a01b-70947635c67b/GCF_014199955.1_ASM1419995v1_genomic.fna.gz | prodigal -d GCF_014199955.1_ASM1419995v1_genomic.fna/cds.fna -a GCF_014199955.1_ASM1419995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:43,553] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:43,553] [INFO] Task started: HMMsearch
[2024-01-24 11:20:43,553] [INFO] Running command: hmmsearch --tblout GCF_014199955.1_ASM1419995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/reference_markers.hmm GCF_014199955.1_ASM1419995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:43,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:43,818] [INFO] Found 6/6 markers.
[2024-01-24 11:20:43,849] [INFO] Query marker FASTA was written to GCF_014199955.1_ASM1419995v1_genomic.fna/markers.fasta
[2024-01-24 11:20:43,850] [INFO] Task started: Blastn
[2024-01-24 11:20:43,850] [INFO] Running command: blastn -query GCF_014199955.1_ASM1419995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/reference_markers.fasta -out GCF_014199955.1_ASM1419995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:44,744] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:44,747] [INFO] Selected 10 target genomes.
[2024-01-24 11:20:44,748] [INFO] Target genome list was writen to GCF_014199955.1_ASM1419995v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:44,789] [INFO] Task started: fastANI
[2024-01-24 11:20:44,790] [INFO] Running command: fastANI --query /var/lib/cwl/stga95bc51b-a8e7-4065-a01b-70947635c67b/GCF_014199955.1_ASM1419995v1_genomic.fna.gz --refList GCF_014199955.1_ASM1419995v1_genomic.fna/target_genomes.txt --output GCF_014199955.1_ASM1419995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:52,844] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:52,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:52,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:52,857] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:52,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:52,858] [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	100.0	1081	1084	95	conclusive
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	87.91	837	1084	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	85.771	799	1084	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	85.3855	774	1084	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.7938	748	1084	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	84.2696	759	1084	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	82.0723	599	1084	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5733	544	1084	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.9852	373	1084	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0953	389	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,859] [INFO] DFAST Taxonomy check result was written to GCF_014199955.1_ASM1419995v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:52,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:52,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:52,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/checkm_data
[2024-01-24 11:20:52,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:52,893] [INFO] Task started: CheckM
[2024-01-24 11:20:52,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199955.1_ASM1419995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199955.1_ASM1419995v1_genomic.fna/checkm_input GCF_014199955.1_ASM1419995v1_genomic.fna/checkm_result
[2024-01-24 11:21:21,281] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:21,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:21,301] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:21,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:21,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199955.1_ASM1419995v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:21,302] [INFO] Task started: Blastn
[2024-01-24 11:21:21,303] [INFO] Running command: blastn -query GCF_014199955.1_ASM1419995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af49e23-ad52-43f6-8bf9-494a71b13157/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199955.1_ASM1419995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:23,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:23,043] [INFO] Selected 12 target genomes.
[2024-01-24 11:21:23,043] [INFO] Target genome list was writen to GCF_014199955.1_ASM1419995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:23,056] [INFO] Task started: fastANI
[2024-01-24 11:21:23,057] [INFO] Running command: fastANI --query /var/lib/cwl/stga95bc51b-a8e7-4065-a01b-70947635c67b/GCF_014199955.1_ASM1419995v1_genomic.fna.gz --refList GCF_014199955.1_ASM1419995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199955.1_ASM1419995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:32,676] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:32,689] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:32,689] [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	100.0	1081	1084	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	89.4517	656	1084	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	88.1399	843	1084	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	87.9261	836	1084	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	87.0763	825	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157625.1	s__Brevundimonas sp002157625	86.0169	765	1084	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	85.9887	819	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248965.1	s__Brevundimonas sp003248965	85.8424	779	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.48	95.48	0.80	0.80	2	-
GCF_902506205.1	s__Brevundimonas sp902506205	85.7021	780	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335735.1	s__Brevundimonas sp000335735	85.5214	757	1084	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	85.51	728	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	85.3372	790	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:32,691] [INFO] GTDB search result was written to GCF_014199955.1_ASM1419995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:32,691] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:32,694] [INFO] DFAST_QC result json was written to GCF_014199955.1_ASM1419995v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:32,694] [INFO] DFAST_QC completed!
[2024-01-24 11:21:32,694] [INFO] Total running time: 0h0m59s