[2024-01-24 12:29:52,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference
[2024-01-24 12:29:53,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,638] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,638] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5c00372-256a-4a5f-903d-15d92323a7e8/GCF_003350205.1_ASM335020v1_genomic.fna.gz | prodigal -d GCF_003350205.1_ASM335020v1_genomic.fna/cds.fna -a GCF_003350205.1_ASM335020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:02,079] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:02,080] [INFO] Task started: HMMsearch
[2024-01-24 12:30:02,080] [INFO] Running command: hmmsearch --tblout GCF_003350205.1_ASM335020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/reference_markers.hmm GCF_003350205.1_ASM335020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:02,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:02,350] [INFO] Found 6/6 markers.
[2024-01-24 12:30:02,384] [INFO] Query marker FASTA was written to GCF_003350205.1_ASM335020v1_genomic.fna/markers.fasta
[2024-01-24 12:30:02,384] [INFO] Task started: Blastn
[2024-01-24 12:30:02,384] [INFO] Running command: blastn -query GCF_003350205.1_ASM335020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/reference_markers.fasta -out GCF_003350205.1_ASM335020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:03,263] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:03,268] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:03,269] [INFO] Target genome list was writen to GCF_003350205.1_ASM335020v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:03,278] [INFO] Task started: fastANI
[2024-01-24 12:30:03,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c00372-256a-4a5f-903d-15d92323a7e8/GCF_003350205.1_ASM335020v1_genomic.fna.gz --refList GCF_003350205.1_ASM335020v1_genomic.fna/target_genomes.txt --output GCF_003350205.1_ASM335020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:14,574] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:14,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:14,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:14,598] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:14,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:14,599] [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 bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	100.0	1093	1096	95	conclusive
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	89.576	869	1096	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	86.1224	771	1096	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	86.1156	790	1096	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	85.6423	708	1096	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	82.8683	671	1096	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	82.7467	691	1096	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.7097	684	1096	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	82.3351	636	1096	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.9572	674	1096	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.4126	612	1096	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.3525	531	1096	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.9571	502	1096	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.2359	393	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:14,600] [INFO] DFAST Taxonomy check result was written to GCF_003350205.1_ASM335020v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:14,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:14,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:14,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/checkm_data
[2024-01-24 12:30:14,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:14,636] [INFO] Task started: CheckM
[2024-01-24 12:30:14,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350205.1_ASM335020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350205.1_ASM335020v1_genomic.fna/checkm_input GCF_003350205.1_ASM335020v1_genomic.fna/checkm_result
[2024-01-24 12:30:43,856] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:43,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:43,878] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:43,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:43,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350205.1_ASM335020v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:43,879] [INFO] Task started: Blastn
[2024-01-24 12:30:43,879] [INFO] Running command: blastn -query GCF_003350205.1_ASM335020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92355c67-6305-4aed-96d9-2c6c2c370cc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350205.1_ASM335020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:45,531] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:45,535] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:45,535] [INFO] Target genome list was writen to GCF_003350205.1_ASM335020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:45,543] [INFO] Task started: fastANI
[2024-01-24 12:30:45,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c00372-256a-4a5f-903d-15d92323a7e8/GCF_003350205.1_ASM335020v1_genomic.fna.gz --refList GCF_003350205.1_ASM335020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350205.1_ASM335020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:53,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:53,581] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:53,581] [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_003350205.1	s__Brevundimonas bullata	100.0	1093	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.07	95.78	0.81	0.78	3	conclusive
GCF_014207965.1	s__Brevundimonas bullata_A	92.1869	866	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002479495.1	s__Brevundimonas sp002479495	90.2211	800	1096	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	89.9001	838	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCF_017487345.1	s__Brevundimonas sp017487345	89.576	869	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387245.1	s__Brevundimonas sp002387245	89.1174	814	1096	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	83.1218	683	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_004614235.1	s__Brevundimonas intermedia	82.9665	686	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196125.1	s__Brevundimonas mediterranea	82.8432	675	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:53,583] [INFO] GTDB search result was written to GCF_003350205.1_ASM335020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:53,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:53,593] [INFO] DFAST_QC result json was written to GCF_003350205.1_ASM335020v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:53,593] [INFO] DFAST_QC completed!
[2024-01-24 12:30:53,593] [INFO] Total running time: 0h1m1s