[2024-01-24 12:21:57,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference
[2024-01-24 12:21:58,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,979] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg00c8df80-5bd1-46ef-bc7a-c8b3f1ba2fa6/GCF_000015445.1_ASM1544v1_genomic.fna.gz | prodigal -d GCF_000015445.1_ASM1544v1_genomic.fna/cds.fna -a GCF_000015445.1_ASM1544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:02,184] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:02,184] [INFO] Task started: HMMsearch
[2024-01-24 12:22:02,184] [INFO] Running command: hmmsearch --tblout GCF_000015445.1_ASM1544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/reference_markers.hmm GCF_000015445.1_ASM1544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:02,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:02,422] [INFO] Found 6/6 markers.
[2024-01-24 12:22:02,454] [INFO] Query marker FASTA was written to GCF_000015445.1_ASM1544v1_genomic.fna/markers.fasta
[2024-01-24 12:22:02,454] [INFO] Task started: Blastn
[2024-01-24 12:22:02,454] [INFO] Running command: blastn -query GCF_000015445.1_ASM1544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/reference_markers.fasta -out GCF_000015445.1_ASM1544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:03,165] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:03,169] [INFO] Selected 24 target genomes.
[2024-01-24 12:22:03,169] [INFO] Target genome list was writen to GCF_000015445.1_ASM1544v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:03,407] [INFO] Task started: fastANI
[2024-01-24 12:22:03,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c8df80-5bd1-46ef-bc7a-c8b3f1ba2fa6/GCF_000015445.1_ASM1544v1_genomic.fna.gz --refList GCF_000015445.1_ASM1544v1_genomic.fna/target_genomes.txt --output GCF_000015445.1_ASM1544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:11,448] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:11,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:11,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:11,466] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:11,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:11,467] [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 bacilliformis	strain=KC583; ATCC 35685	GCA_000015445.1	774	774	type	True	100.0	477	481	95	conclusive
Bartonella schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	80.5732	350	481	95	below_threshold
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	80.5199	342	481	95	below_threshold
Bartonella schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	80.3946	355	481	95	below_threshold
Bartonella bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	80.3156	341	481	95	below_threshold
Bartonella clarridgeiae	strain=ATCC 51734	GCA_000518185.1	56426	56426	type	True	80.0637	304	481	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	79.6537	294	481	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	79.643	289	481	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	79.6198	299	481	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	79.6115	293	481	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	79.5754	280	481	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	79.569	283	481	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	79.5226	280	481	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	79.5117	289	481	95	below_threshold
Bartonella rochalimae	strain=ATCC BAA-1498	GCA_000706645.1	395923	395923	type	True	79.5085	316	481	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	79.4872	301	481	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	79.4724	274	481	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	79.3308	279	481	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	79.2153	281	481	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	79.0861	286	481	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	79.0471	258	481	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	79.0225	262	481	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	78.967	224	481	95	below_threshold
Bartonella australis	strain=AUST/NH1	GCA_000341355.1	388640	388640	type	True	78.4411	246	481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:11,469] [INFO] DFAST Taxonomy check result was written to GCF_000015445.1_ASM1544v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:11,469] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:11,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:11,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/checkm_data
[2024-01-24 12:22:11,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:11,486] [INFO] Task started: CheckM
[2024-01-24 12:22:11,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015445.1_ASM1544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015445.1_ASM1544v1_genomic.fna/checkm_input GCF_000015445.1_ASM1544v1_genomic.fna/checkm_result
[2024-01-24 12:22:30,599] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:30,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.06%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:30,652] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:30,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:30,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015445.1_ASM1544v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:30,652] [INFO] Task started: Blastn
[2024-01-24 12:22:30,653] [INFO] Running command: blastn -query GCF_000015445.1_ASM1544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91496ad-6e9a-4c41-9834-d2a19abe6b5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015445.1_ASM1544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:31,721] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:31,724] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:31,724] [INFO] Target genome list was writen to GCF_000015445.1_ASM1544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:31,735] [INFO] Task started: fastANI
[2024-01-24 12:22:31,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c8df80-5bd1-46ef-bc7a-c8b3f1ba2fa6/GCF_000015445.1_ASM1544v1_genomic.fna.gz --refList GCF_000015445.1_ASM1544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015445.1_ASM1544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:37,616] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:37,630] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:37,630] [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_000015445.1	s__Bartonella bacilliformis	100.0	477	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.64	99.04	0.99	0.96	16	conclusive
GCF_000709795.1	s__Bartonella bacilliformis_A	94.6193	445	481	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	80.6191	351	481	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	80.578	341	481	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	80.5452	337	481	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_000278255.1	s__Bartonella melophagi	80.533	338	481	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	80.3859	350	481	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	80.108	305	481	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	79.9195	314	481	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_000278135.1	s__Bartonella washoeensis	79.7895	299	481	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	79.6198	299	481	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_009936175.1	s__Bartonella quintana	79.5634	300	481	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_000278155.1	s__Bartonella doshiae	79.5515	284	481	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	-
GCF_000046705.1	s__Bartonella henselae	79.5438	293	481	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_000706645.1	s__Bartonella rochalimae	79.4268	315	481	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	-
GCF_902825145.1	s__Bartonella phoceensis	79.3308	279	481	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_000341355.1	s__Bartonella australis	78.4411	246	481	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,633] [INFO] GTDB search result was written to GCF_000015445.1_ASM1544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:37,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:37,640] [INFO] DFAST_QC result json was written to GCF_000015445.1_ASM1544v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:37,640] [INFO] DFAST_QC completed!
[2024-01-24 12:22:37,640] [INFO] Total running time: 0h0m40s