[2024-01-24 13:12:56,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,147] [INFO] DQC Reference Directory: /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference
[2024-01-24 13:12:57,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,539] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg60c83515-5f4d-45ce-a424-52e29759ca63/GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna.gz | prodigal -d GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/cds.fna -a GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:01,088] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:01,089] [INFO] Task started: HMMsearch
[2024-01-24 13:13:01,089] [INFO] Running command: hmmsearch --tblout GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/reference_markers.hmm GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:01,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:01,346] [INFO] Found 6/6 markers.
[2024-01-24 13:13:01,362] [INFO] Query marker FASTA was written to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/markers.fasta
[2024-01-24 13:13:01,362] [INFO] Task started: Blastn
[2024-01-24 13:13:01,363] [INFO] Running command: blastn -query GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/markers.fasta -db /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/reference_markers.fasta -out GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:02,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:02,032] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:02,033] [INFO] Target genome list was writen to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/target_genomes.txt
[2024-01-24 13:13:02,053] [INFO] Task started: fastANI
[2024-01-24 13:13:02,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c83515-5f4d-45ce-a424-52e29759ca63/GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna.gz --refList GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/target_genomes.txt --output GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:06,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:06,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:06,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:06,255] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:13:06,255] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:13:06,255] [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 schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	100.0	506	507	95	inconclusive
Bartonella schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	97.1781	492	507	95	inconclusive
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	96.5143	484	507	95	inconclusive
Bartonella bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	91.0849	467	507	95	below_threshold
Bartonella bovis	strain=91-4	GCA_000384965.1	155194	155194	type	True	91.0035	466	507	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	79.9754	341	507	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	79.954	344	507	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	79.8984	348	507	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	79.2954	325	507	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	78.9398	313	507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:06,257] [INFO] DFAST Taxonomy check result was written to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/tc_result.tsv
[2024-01-24 13:13:06,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:06,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:06,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/checkm_data
[2024-01-24 13:13:06,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:06,289] [INFO] Task started: CheckM
[2024-01-24 13:13:06,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/checkm_input GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/checkm_result
[2024-01-24 13:13:25,124] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:25,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:25,139] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:25,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:25,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/markers.fasta)
[2024-01-24 13:13:25,140] [INFO] Task started: Blastn
[2024-01-24 13:13:25,140] [INFO] Running command: blastn -query GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/markers.fasta -db /var/lib/cwl/stga72df11d-67ea-45b2-bb91-722a4c7a9bfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:26,265] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:26,268] [INFO] Selected 6 target genomes.
[2024-01-24 13:13:26,268] [INFO] Target genome list was writen to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:26,276] [INFO] Task started: fastANI
[2024-01-24 13:13:26,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c83515-5f4d-45ce-a424-52e29759ca63/GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna.gz --refList GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/target_genomes_gtdb.txt --output GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:29,116] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:29,126] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:13:29,127] [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_002022685.1	s__Bartonella schoenbuchensis	97.1781	492	507	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	inconclusive
GCF_000278255.1	s__Bartonella melophagi	95.0306	472	507	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	inconclusive
GCF_002022415.1	s__Bartonella sp002022415	94.229	494	507	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	92.6048	477	507	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_000384965.1	s__Bartonella bovis	91.018	465	507	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	-
GCF_000278135.1	s__Bartonella washoeensis	80.5639	344	507	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:29,131] [INFO] GTDB search result was written to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:29,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:29,137] [INFO] DFAST_QC result json was written to GCF_902810545.1_Bartonella_schoenbuchensis_CCUG50783_genomic.fna/dqc_result.json
[2024-01-24 13:13:29,138] [INFO] DFAST_QC completed!
[2024-01-24 13:13:29,138] [INFO] Total running time: 0h0m33s