[2024-01-24 10:58:18,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:18,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:18,061] [INFO] DQC Reference Directory: /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference
[2024-01-24 10:58:19,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:19,271] [INFO] Task started: Prodigal
[2024-01-24 10:58:19,272] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaacfb90-4692-4a7b-8576-d161d583f45b/GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna.gz | prodigal -d GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/cds.fna -a GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:22,371] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:22,372] [INFO] Task started: HMMsearch
[2024-01-24 10:58:22,372] [INFO] Running command: hmmsearch --tblout GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/reference_markers.hmm GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:22,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:22,589] [INFO] Found 6/6 markers.
[2024-01-24 10:58:22,606] [INFO] Query marker FASTA was written to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/markers.fasta
[2024-01-24 10:58:22,607] [INFO] Task started: Blastn
[2024-01-24 10:58:22,607] [INFO] Running command: blastn -query GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/reference_markers.fasta -out GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:23,251] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:23,255] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:23,255] [INFO] Target genome list was writen to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:23,304] [INFO] Task started: fastANI
[2024-01-24 10:58:23,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaacfb90-4692-4a7b-8576-d161d583f45b/GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna.gz --refList GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/target_genomes.txt --output GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:29,932] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:29,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:29,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:30,004] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:30,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:30,005] [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 rochalimae	strain=ATCC BAA-1498	GCA_000706645.1	395923	395923	type	True	99.9841	501	510	95	conclusive
Bartonella clarridgeiae	strain=ATCC 51734	GCA_000518185.1	56426	56426	type	True	88.6	446	510	95	below_threshold
Bartonella schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	80.0722	335	510	95	below_threshold
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	80.0531	329	510	95	below_threshold
Bartonella bovis	strain=91-4	GCA_000384965.1	155194	155194	type	True	79.9423	338	510	95	below_threshold
Bartonella schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	79.8689	344	510	95	below_threshold
Bartonella bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	79.8678	331	510	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	79.3829	314	510	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	79.3519	318	510	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	79.3485	317	510	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	79.3108	308	510	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	79.1623	309	510	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	79.1568	316	510	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	79.1306	312	510	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	78.9588	308	510	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000312605.2	270250	270250	type	True	78.7553	268	510	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	78.692	317	510	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000278215.1	270250	270250	type	True	78.6771	277	510	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	78.6697	253	510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,007] [INFO] DFAST Taxonomy check result was written to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:30,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:30,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:30,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/checkm_data
[2024-01-24 10:58:30,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:30,030] [INFO] Task started: CheckM
[2024-01-24 10:58:30,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/checkm_input GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/checkm_result
[2024-01-24 10:58:49,513] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:49,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:49,534] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:49,534] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:49,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/markers.fasta)
[2024-01-24 10:58:49,539] [INFO] Task started: Blastn
[2024-01-24 10:58:49,540] [INFO] Running command: blastn -query GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stga95dcb14-0fc6-4f54-922e-a75b0f1749ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:50,900] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:50,903] [INFO] Selected 9 target genomes.
[2024-01-24 10:58:50,903] [INFO] Target genome list was writen to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:50,915] [INFO] Task started: fastANI
[2024-01-24 10:58:50,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaacfb90-4692-4a7b-8576-d161d583f45b/GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna.gz --refList GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:54,653] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:54,677] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:54,677] [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_000706645.1	s__Bartonella rochalimae	99.984	500	510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.99	96.20	0.98	0.97	8	conclusive
GCF_002022445.1	s__Bartonella sp002022445	90.5147	470	510	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_000518185.1	s__Bartonella clarridgeiae	88.6231	447	510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002022665.1	s__Bartonella sp002022665	87.66	445	510	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_002022505.1	s__Bartonella sp002022505	80.1431	327	510	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_002022415.1	s__Bartonella sp002022415	80.01	332	510	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	79.4362	314	510	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_000278235.1	s__Bartonella arupensis	79.1568	316	510	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_000278215.1	s__Bartonella rattimassiliensis	78.6983	275	510	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,679] [INFO] GTDB search result was written to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:54,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:54,683] [INFO] DFAST_QC result json was written to GCF_000706645.1_Bart_roch_BMGH_V1_genomic.fna/dqc_result.json
[2024-01-24 10:58:54,684] [INFO] DFAST_QC completed!
[2024-01-24 10:58:54,684] [INFO] Total running time: 0h0m37s