[2024-01-24 15:26:04,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stga3dcb265-2a17-4a3c-b5e2-9330d876960c/GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna.gz | prodigal -d GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/cds.fna -a GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:11,717] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:11,718] [INFO] Task started: HMMsearch
[2024-01-24 15:26:11,718] [INFO] Running command: hmmsearch --tblout GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/reference_markers.hmm GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:12,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:12,064] [INFO] Found 6/6 markers.
[2024-01-24 15:26:12,087] [INFO] Query marker FASTA was written to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/markers.fasta
[2024-01-24 15:26:12,089] [INFO] Task started: Blastn
[2024-01-24 15:26:12,089] [INFO] Running command: blastn -query GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/markers.fasta -db /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/reference_markers.fasta -out GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:14,799] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:14,802] [INFO] Selected 15 target genomes.
[2024-01-24 15:26:14,803] [INFO] Target genome list was writen to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/target_genomes.txt
[2024-01-24 15:26:14,811] [INFO] Task started: fastANI
[2024-01-24 15:26:14,811] [INFO] Running command: fastANI --query /var/lib/cwl/stga3dcb265-2a17-4a3c-b5e2-9330d876960c/GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna.gz --refList GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/target_genomes.txt --output GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:21,399] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:21,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:21,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:21,419] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:26:21,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:26:21,419] [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
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	93.8002	527	616	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	93.6908	521	616	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	92.8111	527	616	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	92.794	540	616	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	85.4775	537	616	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	84.8889	486	616	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	84.4325	497	616	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.1978	483	616	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.1631	486	616	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.1064	485	616	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	84.0508	492	616	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	83.5236	484	616	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	82.7148	503	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:21,421] [INFO] DFAST Taxonomy check result was written to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/tc_result.tsv
[2024-01-24 15:26:21,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:21,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:21,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/checkm_data
[2024-01-24 15:26:21,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:21,449] [INFO] Task started: CheckM
[2024-01-24 15:26:21,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/checkm_input GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/checkm_result
[2024-01-24 15:26:43,099] [INFO] Task succeeded: CheckM
[2024-01-24 15:26:43,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:26:43,125] [INFO] ===== Completeness check finished =====
[2024-01-24 15:26:43,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:26:43,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/markers.fasta)
[2024-01-24 15:26:43,126] [INFO] Task started: Blastn
[2024-01-24 15:26:43,126] [INFO] Running command: blastn -query GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/markers.fasta -db /var/lib/cwl/stg22af1d5d-152b-4244-afba-4ecbcdb4bc93/dqc_reference/reference_markers_gtdb.fasta -out GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:43,959] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:43,962] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:43,963] [INFO] Target genome list was writen to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:26:43,975] [INFO] Task started: fastANI
[2024-01-24 15:26:43,975] [INFO] Running command: fastANI --query /var/lib/cwl/stga3dcb265-2a17-4a3c-b5e2-9330d876960c/GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna.gz --refList GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/target_genomes_gtdb.txt --output GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:26:51,250] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:51,269] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:26:51,270] [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_902825235.1	s__Bartonella vinsonii	100.0	614	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_902825225.1	s__Bartonella berkhoffii	93.7917	527	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.74	99.27	0.97	0.95	4	-
GCF_000278235.1	s__Bartonella arupensis	92.8147	540	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.53	99.17	0.97	0.95	3	-
GCF_902825155.1	s__Bartonella taylorii_A	86.0969	508	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278295.1	s__Bartonella taylorii	85.9033	521	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.74	97.76	0.94	0.92	5	-
GCF_014203215.1	s__Bartonella callosciuri	84.9337	469	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825145.1	s__Bartonella phoceensis	84.8795	487	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000273375.1	s__Bartonella birtlesii	84.4346	497	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.71	99.25	0.98	0.95	6	-
GCF_000278135.1	s__Bartonella washoeensis	84.3203	501	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.94	98.02	0.92	0.91	3	-
GCF_000046705.1	s__Bartonella henselae	84.075	490	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.52	98.81	0.98	0.94	29	-
GCF_009936175.1	s__Bartonella quintana	84.0111	442	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.46	98.37	0.99	0.97	18	-
GCF_000518085.1	s__Bartonella grahamii	83.9802	503	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.67	99.54	0.97	0.95	5	-
GCF_000706625.1	s__Bartonella koehlerae	83.7037	462	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000278155.1	s__Bartonella doshiae	83.5235	484	616	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.97	97.90	0.96	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 15:26:51,272] [INFO] GTDB search result was written to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/result_gtdb.tsv
[2024-01-24 15:26:51,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:26:51,277] [INFO] DFAST_QC result json was written to GCF_902825235.1_Bartonella_vinsonii_subsp_vinsonii_CIP_103738_genomic.fna/dqc_result.json
[2024-01-24 15:26:51,277] [INFO] DFAST_QC completed!
[2024-01-24 15:26:51,277] [INFO] Total running time: 0h0m47s