[2024-01-25 20:22:50,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference
[2024-01-25 20:22:51,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,822] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg4038656b-3ff9-45cf-afe9-5c7176e5e875/GCF_000092285.1_ASM9228v1_genomic.fna.gz | prodigal -d GCF_000092285.1_ASM9228v1_genomic.fna/cds.fna -a GCF_000092285.1_ASM9228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:02,719] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:02,720] [INFO] Task started: HMMsearch
[2024-01-25 20:23:02,720] [INFO] Running command: hmmsearch --tblout GCF_000092285.1_ASM9228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/reference_markers.hmm GCF_000092285.1_ASM9228v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:02,951] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:02,952] [INFO] Found 6/6 markers.
[2024-01-25 20:23:02,993] [INFO] Query marker FASTA was written to GCF_000092285.1_ASM9228v1_genomic.fna/markers.fasta
[2024-01-25 20:23:02,993] [INFO] Task started: Blastn
[2024-01-25 20:23:02,993] [INFO] Running command: blastn -query GCF_000092285.1_ASM9228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/reference_markers.fasta -out GCF_000092285.1_ASM9228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:03,914] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:03,916] [INFO] Selected 12 target genomes.
[2024-01-25 20:23:03,916] [INFO] Target genome list was writen to GCF_000092285.1_ASM9228v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:03,922] [INFO] Task started: fastANI
[2024-01-25 20:23:03,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg4038656b-3ff9-45cf-afe9-5c7176e5e875/GCF_000092285.1_ASM9228v1_genomic.fna.gz --refList GCF_000092285.1_ASM9228v1_genomic.fna/target_genomes.txt --output GCF_000092285.1_ASM9228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:17,790] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:17,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:17,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:17,799] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:23:17,800] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:17,800] [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
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	100.0	1549	1551	95	conclusive
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	99.9961	1549	1551	95	conclusive
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	85.959	996	1551	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	83.9029	982	1551	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	83.7652	987	1551	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	83.7643	987	1551	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	83.7589	979	1551	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	83.4072	1009	1551	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.3797	650	1551	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.0556	573	1551	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.7187	481	1551	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	78.0578	286	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:17,802] [INFO] DFAST Taxonomy check result was written to GCF_000092285.1_ASM9228v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:17,803] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:17,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:17,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/checkm_data
[2024-01-25 20:23:17,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:17,848] [INFO] Task started: CheckM
[2024-01-25 20:23:17,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092285.1_ASM9228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092285.1_ASM9228v1_genomic.fna/checkm_input GCF_000092285.1_ASM9228v1_genomic.fna/checkm_result
[2024-01-25 20:23:50,615] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:50,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:50,636] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:50,636] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:50,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092285.1_ASM9228v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:50,637] [INFO] Task started: Blastn
[2024-01-25 20:23:50,637] [INFO] Running command: blastn -query GCF_000092285.1_ASM9228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fea9c08-3da6-4462-8c6a-80920fe48230/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092285.1_ASM9228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:52,501] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:52,505] [INFO] Selected 11 target genomes.
[2024-01-25 20:23:52,505] [INFO] Target genome list was writen to GCF_000092285.1_ASM9228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:52,530] [INFO] Task started: fastANI
[2024-01-25 20:23:52,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg4038656b-3ff9-45cf-afe9-5c7176e5e875/GCF_000092285.1_ASM9228v1_genomic.fna.gz --refList GCF_000092285.1_ASM9228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092285.1_ASM9228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:06,693] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:06,701] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:06,701] [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_000092285.1	s__Caulobacter segnis	100.0	1549	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001556515.1	s__Caulobacter sp001556515	90.3033	1054	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742635.1	s__Caulobacter sp002742635	90.1851	1228	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002737755.1	s__Caulobacter sp002737755	89.6786	1155	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243465.1	s__Caulobacter segnis_A	89.3239	1113	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744445.1	s__Caulobacter sp017744445	86.4848	1121	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931565.1	s__Caulobacter sp003931565	86.4672	1132	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207215.1	s__Caulobacter sp014207215	86.1834	1082	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372645.1	s__Caulobacter vibrioides_E	85.9559	1031	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.89	97.90	0.89	0.86	5	-
GCF_002858865.1	s__Caulobacter vibrioides	85.9476	997	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.80	98.06	0.96	0.95	6	-
GCF_002310375.3	s__Caulobacter vibrioides_D	85.9299	1043	1551	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:06,702] [INFO] GTDB search result was written to GCF_000092285.1_ASM9228v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:06,703] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:06,706] [INFO] DFAST_QC result json was written to GCF_000092285.1_ASM9228v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:06,706] [INFO] DFAST_QC completed!
[2024-01-25 20:24:06,706] [INFO] Total running time: 0h1m16s