[2024-01-25 17:42:35,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:35,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:35,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference
[2024-01-25 17:42:36,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:36,658] [INFO] Task started: Prodigal
[2024-01-25 17:42:36,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgda7ca77b-5419-4977-b089-5b6b8b41e739/GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna.gz | prodigal -d GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/cds.fna -a GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:40,344] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:40,345] [INFO] Task started: HMMsearch
[2024-01-25 17:42:40,345] [INFO] Running command: hmmsearch --tblout GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/reference_markers.hmm GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:40,545] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:40,546] [INFO] Found 6/6 markers.
[2024-01-25 17:42:40,573] [INFO] Query marker FASTA was written to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/markers.fasta
[2024-01-25 17:42:40,573] [INFO] Task started: Blastn
[2024-01-25 17:42:40,573] [INFO] Running command: blastn -query GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/reference_markers.fasta -out GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:41,180] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:41,183] [INFO] Selected 17 target genomes.
[2024-01-25 17:42:41,183] [INFO] Target genome list was writen to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/target_genomes.txt
[2024-01-25 17:42:41,196] [INFO] Task started: fastANI
[2024-01-25 17:42:41,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7ca77b-5419-4977-b089-5b6b8b41e739/GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna.gz --refList GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/target_genomes.txt --output GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:48,839] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:48,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:48,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:48,851] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:48,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:48,852] [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 phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	100.0	582	583	95	conclusive
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	85.4423	471	583	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	84.9941	458	583	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	84.9495	455	583	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	84.885	457	583	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	84.8387	464	583	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	84.7733	468	583	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	84.7501	478	583	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	84.7479	469	583	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	84.6776	485	583	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	84.3884	479	583	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.3872	486	583	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.3527	481	583	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.3444	487	583	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	84.3195	484	583	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	83.8437	484	583	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.99	412	583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:48,853] [INFO] DFAST Taxonomy check result was written to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/tc_result.tsv
[2024-01-25 17:42:48,853] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:48,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:48,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/checkm_data
[2024-01-25 17:42:48,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:48,879] [INFO] Task started: CheckM
[2024-01-25 17:42:48,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/checkm_input GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/checkm_result
[2024-01-25 17:43:06,058] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:06,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:06,084] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:06,085] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:06,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/markers.fasta)
[2024-01-25 17:43:06,086] [INFO] Task started: Blastn
[2024-01-25 17:43:06,086] [INFO] Running command: blastn -query GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c9fddfa-034e-4f70-8ae2-13ce842c40ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:07,100] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:07,105] [INFO] Selected 13 target genomes.
[2024-01-25 17:43:07,105] [INFO] Target genome list was writen to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:07,122] [INFO] Task started: fastANI
[2024-01-25 17:43:07,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7ca77b-5419-4977-b089-5b6b8b41e739/GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna.gz --refList GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/target_genomes_gtdb.txt --output GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:13,188] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:13,198] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:13,199] [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_902825145.1	s__Bartonella phoceensis	100.0	582	583	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	conclusive
GCF_902825155.1	s__Bartonella taylorii_A	86.0815	521	583	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	85.4704	470	583	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	85.3589	493	583	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_000278235.1	s__Bartonella arupensis	84.9941	458	583	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_902825235.1	s__Bartonella vinsonii	84.8593	482	583	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_013388295.1	s__Bartonella alsatica	84.8387	464	583	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_902825225.1	s__Bartonella berkhoffii	84.7733	468	583	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_000273375.1	s__Bartonella birtlesii	84.7536	477	583	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_000312525.1	s__Bartonella florencae	84.6838	485	583	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_000046705.1	s__Bartonella henselae	84.3573	480	583	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_000706625.1	s__Bartonella koehlerae	83.9403	457	583	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_000312545.1	s__Bartonella senegalensis	83.5765	478	583	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:13,203] [INFO] GTDB search result was written to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:13,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:13,207] [INFO] DFAST_QC result json was written to GCF_902825145.1_Bartonella_phoceencis_CIP_107707_genomic.fna/dqc_result.json
[2024-01-25 17:43:13,208] [INFO] DFAST_QC completed!
[2024-01-25 17:43:13,208] [INFO] Total running time: 0h0m38s