[2024-01-24 12:29:28,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,919] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference
[2024-01-24 12:29:30,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,461] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b9005af-4289-4a8f-a4ad-450f8b978127/GCF_026642495.1_ASM2664249v1_genomic.fna.gz | prodigal -d GCF_026642495.1_ASM2664249v1_genomic.fna/cds.fna -a GCF_026642495.1_ASM2664249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:32,152] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:32,153] [INFO] Task started: HMMsearch
[2024-01-24 12:29:32,153] [INFO] Running command: hmmsearch --tblout GCF_026642495.1_ASM2664249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/reference_markers.hmm GCF_026642495.1_ASM2664249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:32,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:32,404] [INFO] Found 6/6 markers.
[2024-01-24 12:29:32,425] [INFO] Query marker FASTA was written to GCF_026642495.1_ASM2664249v1_genomic.fna/markers.fasta
[2024-01-24 12:29:32,425] [INFO] Task started: Blastn
[2024-01-24 12:29:32,425] [INFO] Running command: blastn -query GCF_026642495.1_ASM2664249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/reference_markers.fasta -out GCF_026642495.1_ASM2664249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:33,672] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:33,675] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:33,676] [INFO] Target genome list was writen to GCF_026642495.1_ASM2664249v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:33,715] [INFO] Task started: fastANI
[2024-01-24 12:29:33,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9005af-4289-4a8f-a4ad-450f8b978127/GCF_026642495.1_ASM2664249v1_genomic.fna.gz --refList GCF_026642495.1_ASM2664249v1_genomic.fna/target_genomes.txt --output GCF_026642495.1_ASM2664249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:35,834] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:35,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:35,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:35,845] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:29:35,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:35,845] [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=20047	GCA_003814405.1	29519	29519	type	True	99.9991	301	301	95	conclusive
Borreliella garinii	strain=CIP 103362	GCA_001922545.1	29519	29519	type	True	99.999	301	301	95	conclusive
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_003814425.1	664662	29519	type	True	97.516	301	301	95	conclusive
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_000196215.1	664662	29519	type	True	97.4895	300	301	95	conclusive
Borreliella afzelii	strain=DSM 10508	GCA_014202295.1	29518	29518	type	True	93.1672	297	301	95	below_threshold
Borreliella mayonii	strain=MN14-1420	GCA_001945665.1	1674146	1674146	type	True	92.6249	300	301	95	below_threshold
Borreliella japonica	strain=ATCC 51557	GCA_900099615.1	34095	34095	type	True	92.503	293	301	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	92.3532	293	301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:35,850] [INFO] DFAST Taxonomy check result was written to GCF_026642495.1_ASM2664249v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:35,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:35,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:35,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/checkm_data
[2024-01-24 12:29:35,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:35,869] [INFO] Task started: CheckM
[2024-01-24 12:29:35,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026642495.1_ASM2664249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026642495.1_ASM2664249v1_genomic.fna/checkm_input GCF_026642495.1_ASM2664249v1_genomic.fna/checkm_result
[2024-01-24 12:29:51,591] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:51,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:51,609] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:51,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:51,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026642495.1_ASM2664249v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:51,610] [INFO] Task started: Blastn
[2024-01-24 12:29:51,611] [INFO] Running command: blastn -query GCF_026642495.1_ASM2664249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc51203d-8e25-4604-b118-9cb9f06f554b/dqc_reference/reference_markers_gtdb.fasta -out GCF_026642495.1_ASM2664249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:52,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:52,589] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:52,589] [INFO] Target genome list was writen to GCF_026642495.1_ASM2664249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:52,598] [INFO] Task started: fastANI
[2024-01-24 12:29:52,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9005af-4289-4a8f-a4ad-450f8b978127/GCF_026642495.1_ASM2664249v1_genomic.fna.gz --refList GCF_026642495.1_ASM2664249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026642495.1_ASM2664249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:55,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:55,439] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:55,440] [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	99.999	301	301	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	93.1672	297	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.29	99.08	0.96	0.92	10	-
GCF_000170955.2	s__Borreliella valaisiana	92.8624	299	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.52	99.04	0.95	0.92	14	-
GCF_008828755.2	s__Borreliella turdi	92.8328	297	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.10	99.04	0.96	0.96	3	-
GCF_001945665.1	s__Borreliella mayonii	92.6249	300	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900099615.1	s__Borreliella japonica	92.503	293	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205895.1	s__Borreliella lanei	92.4934	295	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008685.2	s__Borreliella burgdorferi	92.3336	296	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	-
GCF_000222305.1	s__Borreliella bissettiae	92.1567	296	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201775.1	s__Borreliella yangtzensis	91.9225	291	301	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:55,442] [INFO] GTDB search result was written to GCF_026642495.1_ASM2664249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:55,442] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:55,445] [INFO] DFAST_QC result json was written to GCF_026642495.1_ASM2664249v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:55,446] [INFO] DFAST_QC completed!
[2024-01-24 12:29:55,446] [INFO] Total running time: 0h0m27s