[2024-01-24 13:17:11,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference
[2024-01-24 13:17:12,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,863] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc9aa37-b80d-4878-a9a5-ac727c4b353e/GCF_001592205.1_ASM159220v1_genomic.fna.gz | prodigal -d GCF_001592205.1_ASM159220v1_genomic.fna/cds.fna -a GCF_001592205.1_ASM159220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:21,635] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:21,635] [INFO] Task started: HMMsearch
[2024-01-24 13:17:21,635] [INFO] Running command: hmmsearch --tblout GCF_001592205.1_ASM159220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/reference_markers.hmm GCF_001592205.1_ASM159220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:21,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:21,875] [INFO] Found 6/6 markers.
[2024-01-24 13:17:21,907] [INFO] Query marker FASTA was written to GCF_001592205.1_ASM159220v1_genomic.fna/markers.fasta
[2024-01-24 13:17:21,907] [INFO] Task started: Blastn
[2024-01-24 13:17:21,907] [INFO] Running command: blastn -query GCF_001592205.1_ASM159220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/reference_markers.fasta -out GCF_001592205.1_ASM159220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:22,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:22,863] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:22,864] [INFO] Target genome list was writen to GCF_001592205.1_ASM159220v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:22,924] [INFO] Task started: fastANI
[2024-01-24 13:17:22,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc9aa37-b80d-4878-a9a5-ac727c4b353e/GCF_001592205.1_ASM159220v1_genomic.fna.gz --refList GCF_001592205.1_ASM159220v1_genomic.fna/target_genomes.txt --output GCF_001592205.1_ASM159220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:33,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:33,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:33,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:33,168] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:33,168] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:33,168] [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 vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	100.0	1095	1097	95	conclusive
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	93.9701	860	1097	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	86.1236	784	1097	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	85.7702	801	1097	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	85.2519	761	1097	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	84.9617	756	1097	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	82.3031	630	1097	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.907	589	1097	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.8072	671	1097	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5651	532	1097	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.3589	397	1097	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.391	398	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:33,170] [INFO] DFAST Taxonomy check result was written to GCF_001592205.1_ASM159220v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:33,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:33,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:33,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/checkm_data
[2024-01-24 13:17:33,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:33,214] [INFO] Task started: CheckM
[2024-01-24 13:17:33,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592205.1_ASM159220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592205.1_ASM159220v1_genomic.fna/checkm_input GCF_001592205.1_ASM159220v1_genomic.fna/checkm_result
[2024-01-24 13:18:03,299] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:03,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:03,324] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:03,324] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:03,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592205.1_ASM159220v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:03,325] [INFO] Task started: Blastn
[2024-01-24 13:18:03,325] [INFO] Running command: blastn -query GCF_001592205.1_ASM159220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11015add-e126-4d6c-ac18-d246759996cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592205.1_ASM159220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:05,178] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:05,181] [INFO] Selected 6 target genomes.
[2024-01-24 13:18:05,182] [INFO] Target genome list was writen to GCF_001592205.1_ASM159220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:05,214] [INFO] Task started: fastANI
[2024-01-24 13:18:05,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc9aa37-b80d-4878-a9a5-ac727c4b353e/GCF_001592205.1_ASM159220v1_genomic.fna.gz --refList GCF_001592205.1_ASM159220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592205.1_ASM159220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:10,431] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:10,442] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:10,443] [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_001592205.1	s__Brevundimonas vesicularis	100.0	1095	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	conclusive
GCF_017086445.1	s__Brevundimonas vesicularis_A	94.3251	882	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	-
GCF_005484585.1	s__Brevundimonas sp005484585	94.3035	871	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	-
GCA_000335735.1	s__Brevundimonas sp000335735	94.1555	850	1097	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	94.1368	858	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813765.1	s__Brevundimonas nasdae_A	93.831	864	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:10,444] [INFO] GTDB search result was written to GCF_001592205.1_ASM159220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:10,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:10,448] [INFO] DFAST_QC result json was written to GCF_001592205.1_ASM159220v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:10,448] [INFO] DFAST_QC completed!
[2024-01-24 13:18:10,448] [INFO] Total running time: 0h0m59s