[2024-01-24 13:46:30,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:30,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:30,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference
[2024-01-24 13:46:31,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:31,330] [INFO] Task started: Prodigal
[2024-01-24 13:46:31,330] [INFO] Running command: gunzip -c /var/lib/cwl/stgf298ea5a-e0ac-4d11-a789-cfec95ba0f53/GCF_014202075.1_ASM1420207v1_genomic.fna.gz | prodigal -d GCF_014202075.1_ASM1420207v1_genomic.fna/cds.fna -a GCF_014202075.1_ASM1420207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:38,288] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:38,288] [INFO] Task started: HMMsearch
[2024-01-24 13:46:38,289] [INFO] Running command: hmmsearch --tblout GCF_014202075.1_ASM1420207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/reference_markers.hmm GCF_014202075.1_ASM1420207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:38,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:38,542] [INFO] Found 6/6 markers.
[2024-01-24 13:46:38,572] [INFO] Query marker FASTA was written to GCF_014202075.1_ASM1420207v1_genomic.fna/markers.fasta
[2024-01-24 13:46:38,572] [INFO] Task started: Blastn
[2024-01-24 13:46:38,572] [INFO] Running command: blastn -query GCF_014202075.1_ASM1420207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/reference_markers.fasta -out GCF_014202075.1_ASM1420207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:39,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:39,544] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:39,544] [INFO] Target genome list was writen to GCF_014202075.1_ASM1420207v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:39,595] [INFO] Task started: fastANI
[2024-01-24 13:46:39,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgf298ea5a-e0ac-4d11-a789-cfec95ba0f53/GCF_014202075.1_ASM1420207v1_genomic.fna.gz --refList GCF_014202075.1_ASM1420207v1_genomic.fna/target_genomes.txt --output GCF_014202075.1_ASM1420207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:48,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:48,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:48,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:48,363] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:48,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:48,363] [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	100.0	879	879	95	conclusive
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	86.0899	719	879	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	84.1947	675	879	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	84.0049	693	879	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.7234	579	879	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	81.5898	560	879	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	81.4412	545	879	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.0263	546	879	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.9112	552	879	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4152	517	879	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.4364	321	879	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.3826	355	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,365] [INFO] DFAST Taxonomy check result was written to GCF_014202075.1_ASM1420207v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:48,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:48,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:48,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/checkm_data
[2024-01-24 13:46:48,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:48,397] [INFO] Task started: CheckM
[2024-01-24 13:46:48,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202075.1_ASM1420207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202075.1_ASM1420207v1_genomic.fna/checkm_input GCF_014202075.1_ASM1420207v1_genomic.fna/checkm_result
[2024-01-24 13:47:14,395] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:14,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:14,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:14,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202075.1_ASM1420207v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:14,417] [INFO] Task started: Blastn
[2024-01-24 13:47:14,417] [INFO] Running command: blastn -query GCF_014202075.1_ASM1420207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg822a816b-660d-42e4-836b-40755b52e52c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202075.1_ASM1420207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:16,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:16,321] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:16,321] [INFO] Target genome list was writen to GCF_014202075.1_ASM1420207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:16,335] [INFO] Task started: fastANI
[2024-01-24 13:47:16,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgf298ea5a-e0ac-4d11-a789-cfec95ba0f53/GCF_014202075.1_ASM1420207v1_genomic.fna.gz --refList GCF_014202075.1_ASM1420207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202075.1_ASM1420207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:23,819] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:23,829] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:23,830] [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_014202075.1	s__Brevundimonas basaltis	100.0	879	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016183935.1	s__Brevundimonas sp016183935	86.653	655	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	86.2907	439	879	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	86.2055	592	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_011927945.1	s__Brevundimonas alba	86.0899	719	879	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	84.9666	648	879	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	84.8309	663	879	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	84.7215	666	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCF_900116065.1	s__Brevundimonas viscosa	84.2073	675	879	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	84.1777	660	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	84.1013	678	879	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 13:47:23,832] [INFO] GTDB search result was written to GCF_014202075.1_ASM1420207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:23,832] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:23,836] [INFO] DFAST_QC result json was written to GCF_014202075.1_ASM1420207v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:23,836] [INFO] DFAST_QC completed!
[2024-01-24 13:47:23,836] [INFO] Total running time: 0h0m54s