[2024-01-24 10:58:17,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:17,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:17,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference
[2024-01-24 10:58:18,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:18,350] [INFO] Task started: Prodigal
[2024-01-24 10:58:18,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f58a3e9-5371-4094-9b68-b290a15f8bc9/GCF_001281405.1_ASM128140v1_genomic.fna.gz | prodigal -d GCF_001281405.1_ASM128140v1_genomic.fna/cds.fna -a GCF_001281405.1_ASM128140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:21,652] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:21,652] [INFO] Task started: HMMsearch
[2024-01-24 10:58:21,653] [INFO] Running command: hmmsearch --tblout GCF_001281405.1_ASM128140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/reference_markers.hmm GCF_001281405.1_ASM128140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:21,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:21,883] [INFO] Found 6/6 markers.
[2024-01-24 10:58:21,909] [INFO] Query marker FASTA was written to GCF_001281405.1_ASM128140v1_genomic.fna/markers.fasta
[2024-01-24 10:58:21,909] [INFO] Task started: Blastn
[2024-01-24 10:58:21,909] [INFO] Running command: blastn -query GCF_001281405.1_ASM128140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/reference_markers.fasta -out GCF_001281405.1_ASM128140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:22,575] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:22,581] [INFO] Selected 23 target genomes.
[2024-01-24 10:58:22,582] [INFO] Target genome list was writen to GCF_001281405.1_ASM128140v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:22,597] [INFO] Task started: fastANI
[2024-01-24 10:58:22,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f58a3e9-5371-4094-9b68-b290a15f8bc9/GCF_001281405.1_ASM128140v1_genomic.fna.gz --refList GCF_001281405.1_ASM128140v1_genomic.fna/target_genomes.txt --output GCF_001281405.1_ASM128140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:32,541] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:32,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:32,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:32,565] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:32,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:32,566] [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 ancashensis	strain=20.00	GCA_001281405.1	1318743	1318743	type	True	100.0	488	489	95	conclusive
Bartonella bacilliformis	strain=KC583; ATCC 35685	GCA_000015445.1	774	774	type	True	79.0196	277	489	95	below_threshold
Bartonella bovis	strain=91-4	GCA_000384965.1	155194	155194	type	True	78.3642	233	489	95	below_threshold
Bartonella schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	78.3318	246	489	95	below_threshold
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	78.2715	232	489	95	below_threshold
Bartonella schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	78.1936	237	489	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	78.1393	192	489	95	below_threshold
Bartonella bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	78.1194	233	489	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	78.0322	196	489	95	below_threshold
Bartonella clarridgeiae	strain=ATCC 51734	GCA_000518185.1	56426	56426	type	True	78.0195	207	489	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	77.9906	189	489	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	77.985	191	489	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	77.741	178	489	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	77.6692	189	489	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	77.5937	187	489	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	77.5841	175	489	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	77.579	207	489	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	77.4374	161	489	95	below_threshold
Bartonella fuyuanensis	strain=DSM 100694	GCA_014197255.1	1460968	1460968	type	True	77.3647	180	489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:32,567] [INFO] DFAST Taxonomy check result was written to GCF_001281405.1_ASM128140v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:32,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:32,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:32,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/checkm_data
[2024-01-24 10:58:32,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:32,589] [INFO] Task started: CheckM
[2024-01-24 10:58:32,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001281405.1_ASM128140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001281405.1_ASM128140v1_genomic.fna/checkm_input GCF_001281405.1_ASM128140v1_genomic.fna/checkm_result
[2024-01-24 10:58:49,979] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:49,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:50,005] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:50,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:50,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001281405.1_ASM128140v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:50,006] [INFO] Task started: Blastn
[2024-01-24 10:58:50,006] [INFO] Running command: blastn -query GCF_001281405.1_ASM128140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745dfd39-567f-49d3-b268-39437aeaab36/dqc_reference/reference_markers_gtdb.fasta -out GCF_001281405.1_ASM128140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:51,026] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:51,033] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:51,033] [INFO] Target genome list was writen to GCF_001281405.1_ASM128140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:51,059] [INFO] Task started: fastANI
[2024-01-24 10:58:51,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f58a3e9-5371-4094-9b68-b290a15f8bc9/GCF_001281405.1_ASM128140v1_genomic.fna.gz --refList GCF_001281405.1_ASM128140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001281405.1_ASM128140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:56,059] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:56,074] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:56,074] [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_001281405.1	s__Bartonella ancashensis	100.0	487	489	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_000709795.1	s__Bartonella bacilliformis_A	79.0922	250	489	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_000015445.1	s__Bartonella bacilliformis	78.9697	277	489	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	-
GCF_002022415.1	s__Bartonella sp002022415	78.4005	229	489	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	78.3984	247	489	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_000384965.1	s__Bartonella bovis	78.2245	231	489	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_002022505.1	s__Bartonella sp002022505	78.2112	243	489	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	78.0896	208	489	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_000278155.1	s__Bartonella doshiae	78.0605	191	489	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_000278115.1	s__Bartonella sp000278115	77.9144	206	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	97.72	97.72	0.97	0.97	2	-
GCF_000312525.1	s__Bartonella florencae	77.6054	185	489	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_903679515.1	s__Bartonella gabonensis	77.5841	175	489	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_014197255.1	s__Bartonella fuyuanensis	77.351	181	489	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 10:58:56,076] [INFO] GTDB search result was written to GCF_001281405.1_ASM128140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:56,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:56,080] [INFO] DFAST_QC result json was written to GCF_001281405.1_ASM128140v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:56,080] [INFO] DFAST_QC completed!
[2024-01-24 10:58:56,080] [INFO] Total running time: 0h0m39s