[2024-01-24 14:39:15,638] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference
[2024-01-24 14:39:18,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,583] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dfc5765-3ba9-407e-be38-08d4bf0617cb/GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna.gz | prodigal -d GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/cds.fna -a GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:23,549] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:23,549] [INFO] Task started: HMMsearch
[2024-01-24 14:39:23,549] [INFO] Running command: hmmsearch --tblout GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/reference_markers.hmm GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:23,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:23,891] [INFO] Found 6/6 markers.
[2024-01-24 14:39:23,918] [INFO] Query marker FASTA was written to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/markers.fasta
[2024-01-24 14:39:23,919] [INFO] Task started: Blastn
[2024-01-24 14:39:23,919] [INFO] Running command: blastn -query GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/reference_markers.fasta -out GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:27,388] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:27,392] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:27,393] [INFO] Target genome list was writen to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/target_genomes.txt
[2024-01-24 14:39:27,478] [INFO] Task started: fastANI
[2024-01-24 14:39:27,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dfc5765-3ba9-407e-be38-08d4bf0617cb/GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna.gz --refList GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/target_genomes.txt --output GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:35,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:35,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:35,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:35,655] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:35,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:35,655] [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	100.0	562	565	95	conclusive
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	99.9345	538	565	95	conclusive
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	92.2376	509	565	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	92.1584	516	565	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	85.2756	505	565	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	84.6849	482	565	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	84.6696	464	565	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.0851	480	565	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.0507	473	565	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.0492	484	565	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	83.9574	481	565	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	83.631	502	565	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.658	402	565	95	below_threshold
Bartonella rochalimae	strain=ATCC BAA-1498	GCA_000706645.1	395923	395923	type	True	79.0681	304	565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,657] [INFO] DFAST Taxonomy check result was written to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/tc_result.tsv
[2024-01-24 14:39:35,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:35,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:35,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/checkm_data
[2024-01-24 14:39:35,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:35,682] [INFO] Task started: CheckM
[2024-01-24 14:39:35,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/checkm_input GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/checkm_result
[2024-01-24 14:40:01,030] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:01,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:01,065] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:01,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:01,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/markers.fasta)
[2024-01-24 14:40:01,066] [INFO] Task started: Blastn
[2024-01-24 14:40:01,066] [INFO] Running command: blastn -query GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2033f4b-073e-424a-95b6-1e683677caf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:02,404] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:02,409] [INFO] Selected 15 target genomes.
[2024-01-24 14:40:02,410] [INFO] Target genome list was writen to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:02,425] [INFO] Task started: fastANI
[2024-01-24 14:40:02,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dfc5765-3ba9-407e-be38-08d4bf0617cb/GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna.gz --refList GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/target_genomes_gtdb.txt --output GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:09,669] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:09,682] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:09,683] [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_902825225.1	s__Bartonella berkhoffii	100.0	562	565	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	conclusive
GCF_902825235.1	s__Bartonella vinsonii	93.7714	532	565	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	-
GCF_000278235.1	s__Bartonella arupensis	92.1584	516	565	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_000278295.1	s__Bartonella taylorii	85.5516	503	565	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_902825145.1	s__Bartonella phoceensis	84.6849	482	565	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_014203215.1	s__Bartonella callosciuri	84.6625	465	565	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_013388295.1	s__Bartonella alsatica	84.519	452	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.98	99.96	0.99	0.99	3	-
GCF_000278135.1	s__Bartonella washoeensis	84.185	493	565	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_000273375.1	s__Bartonella birtlesii	84.059	476	565	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_000046705.1	s__Bartonella henselae	83.9574	481	565	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	83.9463	434	565	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_000312525.1	s__Bartonella florencae	83.9396	478	565	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_000518085.1	s__Bartonella grahamii	83.5948	487	565	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_000312565.1	s__Bartonella rattaustraliani	82.677	446	565	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_000312585.1	s__Bartonella queenslandensis_A	82.2246	472	565	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:09,685] [INFO] GTDB search result was written to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:09,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:09,689] [INFO] DFAST_QC result json was written to GCF_902825225.1_Bartonella_vinsonii_subsp_berkhoffii_CIP_104960_genomic.fna/dqc_result.json
[2024-01-24 14:40:09,690] [INFO] DFAST_QC completed!
[2024-01-24 14:40:09,690] [INFO] Total running time: 0h0m54s