[2024-01-25 19:51:05,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:05,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:05,592] [INFO] DQC Reference Directory: /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference
[2024-01-25 19:51:06,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:06,721] [INFO] Task started: Prodigal
[2024-01-25 19:51:06,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bd41659-4c48-4317-8cbf-ad0261ed7d5e/GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna.gz | prodigal -d GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/cds.fna -a GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:09,831] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:09,831] [INFO] Task started: HMMsearch
[2024-01-25 19:51:09,831] [INFO] Running command: hmmsearch --tblout GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/reference_markers.hmm GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:10,043] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:10,044] [INFO] Found 6/6 markers.
[2024-01-25 19:51:10,059] [INFO] Query marker FASTA was written to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/markers.fasta
[2024-01-25 19:51:10,059] [INFO] Task started: Blastn
[2024-01-25 19:51:10,059] [INFO] Running command: blastn -query GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/markers.fasta -db /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/reference_markers.fasta -out GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:10,668] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:10,671] [INFO] Selected 10 target genomes.
[2024-01-25 19:51:10,672] [INFO] Target genome list was writen to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/target_genomes.txt
[2024-01-25 19:51:10,680] [INFO] Task started: fastANI
[2024-01-25 19:51:10,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bd41659-4c48-4317-8cbf-ad0261ed7d5e/GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna.gz --refList GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/target_genomes.txt --output GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:14,453] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:14,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:14,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:14,463] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:51:14,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:14,463] [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 bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	100.0	492	493	95	conclusive
Bartonella bovis	strain=91-4	GCA_000384965.1	155194	155194	type	True	99.9745	491	493	95	conclusive
Bartonella schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	90.9952	462	493	95	below_threshold
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	90.9884	465	493	95	below_threshold
Bartonella schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	90.8931	476	493	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	80.005	334	493	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	79.9904	330	493	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	79.9541	338	493	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	79.2905	311	493	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	78.8294	268	493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:14,465] [INFO] DFAST Taxonomy check result was written to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/tc_result.tsv
[2024-01-25 19:51:14,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:14,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:14,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/checkm_data
[2024-01-25 19:51:14,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:14,491] [INFO] Task started: CheckM
[2024-01-25 19:51:14,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/checkm_input GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/checkm_result
[2024-01-25 19:51:30,641] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:30,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 25.41%
Strain heterogeneity: 63.64%
--------------------------------------------------------------------------------
[2024-01-25 19:51:30,665] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:30,665] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:30,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/markers.fasta)
[2024-01-25 19:51:30,666] [INFO] Task started: Blastn
[2024-01-25 19:51:30,666] [INFO] Running command: blastn -query GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/markers.fasta -db /var/lib/cwl/stga07105ad-ab95-4616-bc6c-9e08460e39f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:31,625] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:31,629] [INFO] Selected 6 target genomes.
[2024-01-25 19:51:31,629] [INFO] Target genome list was writen to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:31,639] [INFO] Task started: fastANI
[2024-01-25 19:51:31,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bd41659-4c48-4317-8cbf-ad0261ed7d5e/GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna.gz --refList GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/target_genomes_gtdb.txt --output GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:34,119] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:34,124] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:34,124] [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_000384965.1	s__Bartonella bovis	99.9745	491	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	96.94	95.09	0.95	0.93	3	conclusive
GCF_000278255.1	s__Bartonella melophagi	90.9909	452	493	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_002022685.1	s__Bartonella schoenbuchensis	90.8761	476	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	97.27	97.07	0.97	0.95	5	-
GCF_002022415.1	s__Bartonella sp002022415	90.7389	473	493	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_002022505.1	s__Bartonella sp002022505	90.509	475	493	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_000278135.1	s__Bartonella washoeensis	80.3048	343	493	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:34,126] [INFO] GTDB search result was written to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:34,126] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:34,128] [INFO] DFAST_QC result json was written to GCF_902728095.1_Bartonella_bovis_CIP106692_genomic.fna/dqc_result.json
[2024-01-25 19:51:34,129] [INFO] DFAST_QC completed!
[2024-01-25 19:51:34,129] [INFO] Total running time: 0h0m29s