[2024-01-25 18:07:05,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:05,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:05,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference
[2024-01-25 18:07:06,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:06,672] [INFO] Task started: Prodigal
[2024-01-25 18:07:06,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg6258d4ab-d3d8-46fb-b310-8e25053be608/GCF_002022685.1_ASM202268v1_genomic.fna.gz | prodigal -d GCF_002022685.1_ASM202268v1_genomic.fna/cds.fna -a GCF_002022685.1_ASM202268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:10,045] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:10,045] [INFO] Task started: HMMsearch
[2024-01-25 18:07:10,045] [INFO] Running command: hmmsearch --tblout GCF_002022685.1_ASM202268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/reference_markers.hmm GCF_002022685.1_ASM202268v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:10,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:10,248] [INFO] Found 6/6 markers.
[2024-01-25 18:07:10,267] [INFO] Query marker FASTA was written to GCF_002022685.1_ASM202268v1_genomic.fna/markers.fasta
[2024-01-25 18:07:10,267] [INFO] Task started: Blastn
[2024-01-25 18:07:10,267] [INFO] Running command: blastn -query GCF_002022685.1_ASM202268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/reference_markers.fasta -out GCF_002022685.1_ASM202268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:10,872] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:10,875] [INFO] Selected 10 target genomes.
[2024-01-25 18:07:10,875] [INFO] Target genome list was writen to GCF_002022685.1_ASM202268v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:10,882] [INFO] Task started: fastANI
[2024-01-25 18:07:10,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg6258d4ab-d3d8-46fb-b310-8e25053be608/GCF_002022685.1_ASM202268v1_genomic.fna.gz --refList GCF_002022685.1_ASM202268v1_genomic.fna/target_genomes.txt --output GCF_002022685.1_ASM202268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:15,041] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:15,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:15,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:15,049] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:07:15,049] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:07:15,049] [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 schoenbuchensis	strain=R1	GCA_002022685.1	165694	165694	type	True	100.0	575	575	95	inconclusive
Bartonella schoenbuchensis	strain=CCUG 50783	GCA_902810545.1	165694	165694	suspected-type	True	97.1435	499	575	95	inconclusive
Bartonella capreoli	strain=DSM 21569	GCA_902813205.1	155192	155192	type	True	97.0807	496	575	95	inconclusive
Bartonella bovis	strain=CIP 106692	GCA_902728095.1	155194	155194	type	True	90.8472	477	575	95	below_threshold
Bartonella bovis	strain=91-4	GCA_000384965.1	155194	155194	type	True	90.5112	499	575	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	80.0457	348	575	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	80.0059	354	575	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	80.0058	360	575	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	79.2439	329	575	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	79.1705	321	575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:15,051] [INFO] DFAST Taxonomy check result was written to GCF_002022685.1_ASM202268v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:15,052] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:15,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:15,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/checkm_data
[2024-01-25 18:07:15,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:15,073] [INFO] Task started: CheckM
[2024-01-25 18:07:15,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002022685.1_ASM202268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002022685.1_ASM202268v1_genomic.fna/checkm_input GCF_002022685.1_ASM202268v1_genomic.fna/checkm_result
[2024-01-25 18:07:31,202] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:31,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:31,217] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:31,218] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:31,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002022685.1_ASM202268v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:31,218] [INFO] Task started: Blastn
[2024-01-25 18:07:31,218] [INFO] Running command: blastn -query GCF_002022685.1_ASM202268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11df73c6-abd2-45c5-9768-1306de4d5d73/dqc_reference/reference_markers_gtdb.fasta -out GCF_002022685.1_ASM202268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:32,206] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:32,208] [INFO] Selected 6 target genomes.
[2024-01-25 18:07:32,208] [INFO] Target genome list was writen to GCF_002022685.1_ASM202268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:32,211] [INFO] Task started: fastANI
[2024-01-25 18:07:32,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg6258d4ab-d3d8-46fb-b310-8e25053be608/GCF_002022685.1_ASM202268v1_genomic.fna.gz --refList GCF_002022685.1_ASM202268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002022685.1_ASM202268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:35,230] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:35,235] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:35,235] [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_002022685.1	s__Bartonella schoenbuchensis	100.0	575	575	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	conclusive
GCF_000278255.1	s__Bartonella melophagi	94.8048	493	575	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	94.0534	529	575	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	92.2044	520	575	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	90.5624	498	575	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_000278135.1	s__Bartonella washoeensis	80.5225	355	575	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:35,236] [INFO] GTDB search result was written to GCF_002022685.1_ASM202268v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:35,237] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:35,239] [INFO] DFAST_QC result json was written to GCF_002022685.1_ASM202268v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:35,240] [INFO] DFAST_QC completed!
[2024-01-25 18:07:35,240] [INFO] Total running time: 0h0m30s