[2024-01-25 17:48:50,366] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:50,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:50,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference
[2024-01-25 17:48:51,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:51,542] [INFO] Task started: Prodigal
[2024-01-25 17:48:51,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg57da471e-3532-4b3d-a79a-a6aae6c2503e/GCF_001922545.1_ASM192254v1_genomic.fna.gz | prodigal -d GCF_001922545.1_ASM192254v1_genomic.fna/cds.fna -a GCF_001922545.1_ASM192254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:53,232] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:53,232] [INFO] Task started: HMMsearch
[2024-01-25 17:48:53,233] [INFO] Running command: hmmsearch --tblout GCF_001922545.1_ASM192254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/reference_markers.hmm GCF_001922545.1_ASM192254v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:53,405] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:53,406] [INFO] Found 6/6 markers.
[2024-01-25 17:48:53,421] [INFO] Query marker FASTA was written to GCF_001922545.1_ASM192254v1_genomic.fna/markers.fasta
[2024-01-25 17:48:53,421] [INFO] Task started: Blastn
[2024-01-25 17:48:53,421] [INFO] Running command: blastn -query GCF_001922545.1_ASM192254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/reference_markers.fasta -out GCF_001922545.1_ASM192254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:54,015] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:54,018] [INFO] Selected 8 target genomes.
[2024-01-25 17:48:54,018] [INFO] Target genome list was writen to GCF_001922545.1_ASM192254v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:54,027] [INFO] Task started: fastANI
[2024-01-25 17:48:54,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg57da471e-3532-4b3d-a79a-a6aae6c2503e/GCF_001922545.1_ASM192254v1_genomic.fna.gz --refList GCF_001922545.1_ASM192254v1_genomic.fna/target_genomes.txt --output GCF_001922545.1_ASM192254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:56,796] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:56,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:56,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:56,804] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 17:48:56,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:56,804] [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
Borreliella garinii	strain=CIP 103362	GCA_001922545.1	29519	29519	type	True	100.0	380	380	95	conclusive
Borreliella garinii	strain=20047	GCA_003814405.1	29519	29519	type	True	99.9969	378	380	95	conclusive
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_000196215.1	664662	29519	type	True	97.3006	326	380	95	conclusive
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_003814425.1	664662	29519	type	True	96.9295	361	380	95	conclusive
Borreliella afzelii	strain=DSM 10508	GCA_014202295.1	29518	29518	type	True	92.4735	350	380	95	below_threshold
Borreliella japonica	strain=ATCC 51557	GCA_900099615.1	34095	34095	type	True	91.7213	343	380	95	below_threshold
Borreliella mayonii	strain=MN14-1420	GCA_001945665.1	1674146	1674146	type	True	91.6089	352	380	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	91.1246	362	380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:56,805] [INFO] DFAST Taxonomy check result was written to GCF_001922545.1_ASM192254v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:56,806] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:56,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:56,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/checkm_data
[2024-01-25 17:48:56,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:56,822] [INFO] Task started: CheckM
[2024-01-25 17:48:56,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001922545.1_ASM192254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001922545.1_ASM192254v1_genomic.fna/checkm_input GCF_001922545.1_ASM192254v1_genomic.fna/checkm_result
[2024-01-25 17:49:09,257] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:09,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:09,276] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:09,276] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:09,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001922545.1_ASM192254v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:09,277] [INFO] Task started: Blastn
[2024-01-25 17:49:09,277] [INFO] Running command: blastn -query GCF_001922545.1_ASM192254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15e532cb-695f-44aa-96ec-0025041dff12/dqc_reference/reference_markers_gtdb.fasta -out GCF_001922545.1_ASM192254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:10,272] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:10,275] [INFO] Selected 10 target genomes.
[2024-01-25 17:49:10,275] [INFO] Target genome list was writen to GCF_001922545.1_ASM192254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:10,283] [INFO] Task started: fastANI
[2024-01-25 17:49:10,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg57da471e-3532-4b3d-a79a-a6aae6c2503e/GCF_001922545.1_ASM192254v1_genomic.fna.gz --refList GCF_001922545.1_ASM192254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001922545.1_ASM192254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:13,904] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:13,912] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:13,912] [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_001922545.1	s__Borreliella garinii	100.0	380	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	97.97	96.83	0.94	0.85	112	conclusive
GCF_014202295.1	s__Borreliella afzelii	92.5447	348	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.29	99.08	0.96	0.92	10	-
GCF_008828755.2	s__Borreliella turdi	92.3198	341	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.10	99.04	0.96	0.96	3	-
GCF_000170955.2	s__Borreliella valaisiana	92.0757	347	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.52	99.04	0.95	0.92	14	-
GCF_014205895.1	s__Borreliella lanei	91.7684	335	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099615.1	s__Borreliella japonica	91.7525	342	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945665.1	s__Borreliella mayonii	91.6001	353	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000008685.2	s__Borreliella burgdorferi	91.2692	362	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	-
GCF_014201775.1	s__Borreliella yangtzensis	91.0911	343	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222305.1	s__Borreliella bissettiae	91.0009	358	380	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:13,913] [INFO] GTDB search result was written to GCF_001922545.1_ASM192254v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:13,915] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:13,918] [INFO] DFAST_QC result json was written to GCF_001922545.1_ASM192254v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:13,918] [INFO] DFAST_QC completed!
[2024-01-25 17:49:13,918] [INFO] Total running time: 0h0m24s