[2024-01-25 17:35:35,711] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference
[2024-01-25 17:35:36,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,922] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg1956816e-feae-4d32-b41a-8852b7350661/GCF_014201435.1_ASM1420143v1_genomic.fna.gz | prodigal -d GCF_014201435.1_ASM1420143v1_genomic.fna/cds.fna -a GCF_014201435.1_ASM1420143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:40,393] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:40,393] [INFO] Task started: HMMsearch
[2024-01-25 17:35:40,393] [INFO] Running command: hmmsearch --tblout GCF_014201435.1_ASM1420143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/reference_markers.hmm GCF_014201435.1_ASM1420143v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:40,618] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:40,619] [INFO] Found 6/6 markers.
[2024-01-25 17:35:40,635] [INFO] Query marker FASTA was written to GCF_014201435.1_ASM1420143v1_genomic.fna/markers.fasta
[2024-01-25 17:35:40,636] [INFO] Task started: Blastn
[2024-01-25 17:35:40,636] [INFO] Running command: blastn -query GCF_014201435.1_ASM1420143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/reference_markers.fasta -out GCF_014201435.1_ASM1420143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:41,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:41,241] [INFO] Selected 10 target genomes.
[2024-01-25 17:35:41,242] [INFO] Target genome list was writen to GCF_014201435.1_ASM1420143v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:41,245] [INFO] Task started: fastANI
[2024-01-25 17:35:41,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg1956816e-feae-4d32-b41a-8852b7350661/GCF_014201435.1_ASM1420143v1_genomic.fna.gz --refList GCF_014201435.1_ASM1420143v1_genomic.fna/target_genomes.txt --output GCF_014201435.1_ASM1420143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:45,754] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:45,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:45,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:45,762] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:35:45,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:45,762] [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 doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	100.0	567	571	95	conclusive
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	99.9994	570	571	95	conclusive
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	99.9828	570	571	95	conclusive
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	99.9824	557	571	95	conclusive
Bartonella doshiae	strain=CCUG 50770	GCA_902728115.1	33044	33044	type	True	99.9776	567	571	95	conclusive
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	83.1082	470	571	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	83.0955	472	571	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	83.0207	481	571	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	82.3135	456	571	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	81.7722	396	571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:45,764] [INFO] DFAST Taxonomy check result was written to GCF_014201435.1_ASM1420143v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:45,764] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:45,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:45,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/checkm_data
[2024-01-25 17:35:45,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:45,786] [INFO] Task started: CheckM
[2024-01-25 17:35:45,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201435.1_ASM1420143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201435.1_ASM1420143v1_genomic.fna/checkm_input GCF_014201435.1_ASM1420143v1_genomic.fna/checkm_result
[2024-01-25 17:36:02,866] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:02,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:02,882] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:02,883] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:02,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201435.1_ASM1420143v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:02,883] [INFO] Task started: Blastn
[2024-01-25 17:36:02,883] [INFO] Running command: blastn -query GCF_014201435.1_ASM1420143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg961e9680-caf0-4d9b-8d99-376dc9f55853/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201435.1_ASM1420143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:04,006] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:04,009] [INFO] Selected 14 target genomes.
[2024-01-25 17:36:04,009] [INFO] Target genome list was writen to GCF_014201435.1_ASM1420143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:04,020] [INFO] Task started: fastANI
[2024-01-25 17:36:04,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg1956816e-feae-4d32-b41a-8852b7350661/GCF_014201435.1_ASM1420143v1_genomic.fna.gz --refList GCF_014201435.1_ASM1420143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201435.1_ASM1420143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:10,748] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:10,757] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:10,757] [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_000278155.1	s__Bartonella doshiae	99.9828	570	571	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	conclusive
GCF_000278295.1	s__Bartonella taylorii	84.8079	471	571	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_902825155.1	s__Bartonella taylorii_A	84.5601	480	571	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	83.4466	475	571	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_902825235.1	s__Bartonella vinsonii	83.4179	466	571	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_000518085.1	s__Bartonella grahamii	83.2723	473	571	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_009936175.1	s__Bartonella quintana	83.2003	431	571	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_000273375.1	s__Bartonella birtlesii	83.1356	461	571	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	83.0947	461	571	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_000278235.1	s__Bartonella arupensis	83.0795	454	571	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_014203215.1	s__Bartonella callosciuri	83.07	434	571	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_000706625.1	s__Bartonella koehlerae	82.7576	454	571	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_013388295.1	s__Bartonella alsatica	82.7059	427	571	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_014197255.1	s__Bartonella fuyuanensis	81.4277	420	571	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 17:36:10,759] [INFO] GTDB search result was written to GCF_014201435.1_ASM1420143v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:10,759] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:10,762] [INFO] DFAST_QC result json was written to GCF_014201435.1_ASM1420143v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:10,763] [INFO] DFAST_QC completed!
[2024-01-25 17:36:10,763] [INFO] Total running time: 0h0m35s