[2024-01-24 13:09:48,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:48,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:48,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference
[2024-01-24 13:09:50,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,168] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,168] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf203920-e077-4595-b284-27246ac7a10a/GCF_000312545.1_ASM31254v1_genomic.fna.gz | prodigal -d GCF_000312545.1_ASM31254v1_genomic.fna/cds.fna -a GCF_000312545.1_ASM31254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:54,943] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:54,943] [INFO] Task started: HMMsearch
[2024-01-24 13:09:54,943] [INFO] Running command: hmmsearch --tblout GCF_000312545.1_ASM31254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/reference_markers.hmm GCF_000312545.1_ASM31254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:55,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:55,222] [INFO] Found 6/6 markers.
[2024-01-24 13:09:55,248] [INFO] Query marker FASTA was written to GCF_000312545.1_ASM31254v1_genomic.fna/markers.fasta
[2024-01-24 13:09:55,248] [INFO] Task started: Blastn
[2024-01-24 13:09:55,248] [INFO] Running command: blastn -query GCF_000312545.1_ASM31254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/reference_markers.fasta -out GCF_000312545.1_ASM31254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:55,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:55,839] [INFO] Selected 14 target genomes.
[2024-01-24 13:09:55,840] [INFO] Target genome list was writen to GCF_000312545.1_ASM31254v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:55,852] [INFO] Task started: fastANI
[2024-01-24 13:09:55,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf203920-e077-4595-b284-27246ac7a10a/GCF_000312545.1_ASM31254v1_genomic.fna.gz --refList GCF_000312545.1_ASM31254v1_genomic.fna/target_genomes.txt --output GCF_000312545.1_ASM31254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:02,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:02,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:02,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:02,253] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:02,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:02,254] [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 senegalensis	strain=OS02	GCA_000312545.1	1468418	1468418	type	True	99.9997	649	655	95	conclusive
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	89.4521	554	655	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	89.3544	562	655	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	89.351	561	655	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	89.3426	562	655	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	89.3343	555	655	95	below_threshold
Bartonella koehlerae subsp. koehlerae	strain=C-29	GCA_000706625.1	1819240	92181	type	True	88.8776	530	655	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	83.6178	459	655	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	83.4714	466	655	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	83.4452	477	655	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	83.4274	481	655	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	83.3694	476	655	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.6079	430	655	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	82.1706	506	655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:02,255] [INFO] DFAST Taxonomy check result was written to GCF_000312545.1_ASM31254v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:02,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:02,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:02,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/checkm_data
[2024-01-24 13:10:02,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:02,280] [INFO] Task started: CheckM
[2024-01-24 13:10:02,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000312545.1_ASM31254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000312545.1_ASM31254v1_genomic.fna/checkm_input GCF_000312545.1_ASM31254v1_genomic.fna/checkm_result
[2024-01-24 13:10:23,031] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:23,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,051] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:23,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:23,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000312545.1_ASM31254v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:23,052] [INFO] Task started: Blastn
[2024-01-24 13:10:23,052] [INFO] Running command: blastn -query GCF_000312545.1_ASM31254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5df78712-7181-45a8-83a7-8ce3756201d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000312545.1_ASM31254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:23,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:23,831] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:23,831] [INFO] Target genome list was writen to GCF_000312545.1_ASM31254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:23,917] [INFO] Task started: fastANI
[2024-01-24 13:10:23,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf203920-e077-4595-b284-27246ac7a10a/GCF_000312545.1_ASM31254v1_genomic.fna.gz --refList GCF_000312545.1_ASM31254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000312545.1_ASM31254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:29,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:29,955] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:29,956] [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_000312545.1	s__Bartonella senegalensis	99.9997	649	655	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_000046705.1	s__Bartonella henselae	89.4521	554	655	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	88.8776	530	655	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_009936175.1	s__Bartonella quintana	85.3146	466	655	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_000278135.1	s__Bartonella washoeensis	83.9621	497	655	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_000278295.1	s__Bartonella taylorii	83.8583	525	655	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_000312525.1	s__Bartonella florencae	83.7996	510	655	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_013388295.1	s__Bartonella alsatica	83.4714	466	655	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_902825145.1	s__Bartonella phoceensis	83.4452	477	655	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_902825235.1	s__Bartonella vinsonii	83.4206	500	655	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_000273375.1	s__Bartonella birtlesii	83.364	496	655	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_002777915.1	s__Bartonella tribocorum_A	82.3644	503	655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000518165.1	s__Bartonella elizabethae	82.1276	484	655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.20	95.98	0.98	0.96	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:29,958] [INFO] GTDB search result was written to GCF_000312545.1_ASM31254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:29,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:29,965] [INFO] DFAST_QC result json was written to GCF_000312545.1_ASM31254v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:29,965] [INFO] DFAST_QC completed!
[2024-01-24 13:10:29,965] [INFO] Total running time: 0h0m41s