[2024-01-24 12:31:34,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference
[2024-01-24 12:31:35,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,259] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,259] [INFO] Running command: gunzip -c /var/lib/cwl/stga4224b22-eb85-43b3-9d51-76cf45170394/GCF_023035295.1_ASM2303529v1_genomic.fna.gz | prodigal -d GCF_023035295.1_ASM2303529v1_genomic.fna/cds.fna -a GCF_023035295.1_ASM2303529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:38,112] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:38,112] [INFO] Task started: HMMsearch
[2024-01-24 12:31:38,112] [INFO] Running command: hmmsearch --tblout GCF_023035295.1_ASM2303529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/reference_markers.hmm GCF_023035295.1_ASM2303529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:38,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:38,321] [INFO] Found 6/6 markers.
[2024-01-24 12:31:38,342] [INFO] Query marker FASTA was written to GCF_023035295.1_ASM2303529v1_genomic.fna/markers.fasta
[2024-01-24 12:31:38,342] [INFO] Task started: Blastn
[2024-01-24 12:31:38,342] [INFO] Running command: blastn -query GCF_023035295.1_ASM2303529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/reference_markers.fasta -out GCF_023035295.1_ASM2303529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:38,897] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:38,903] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:38,903] [INFO] Target genome list was writen to GCF_023035295.1_ASM2303529v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:38,915] [INFO] Task started: fastANI
[2024-01-24 12:31:38,916] [INFO] Running command: fastANI --query /var/lib/cwl/stga4224b22-eb85-43b3-9d51-76cf45170394/GCF_023035295.1_ASM2303529v1_genomic.fna.gz --refList GCF_023035295.1_ASM2303529v1_genomic.fna/target_genomes.txt --output GCF_023035295.1_ASM2303529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:44,414] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:44,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:44,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:44,431] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:44,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:44,432] [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
Borrelia coriaceae	strain=Co53	GCA_023035295.1	144	144	type	True	100.0	580	583	95	conclusive
Borrelia coriaceae	strain=ATCC 43381	GCA_000518125.1	144	144	type	True	99.8429	481	583	95	conclusive
Borrelia coriaceae	strain=Co53	GCA_000568755.1	144	144	type	True	99.8184	513	583	95	conclusive
Borrelia parkeri	strain=SLO	GCA_000568735.2	141	141	reftype	True	88.7143	299	583	95	below_threshold
Borrelia turicatae	strain=91E135	GCA_000012085.2	142	142	reftype	True	87.5838	355	583	95	below_threshold
Borrelia hermsii	strain=DAH	GCA_000012065.2	140	140	suspected-type	True	87.4233	322	583	95	below_threshold
Borrelia hermsii	strain=DAH	GCA_023035675.1	140	140	suspected-type	True	86.4687	394	583	95	below_threshold
Borrelia puertoricensis	strain=SUM	GCA_023035875.1	2756107	2756107	type	True	86.0435	417	583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:44,434] [INFO] DFAST Taxonomy check result was written to GCF_023035295.1_ASM2303529v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:44,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:44,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:44,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/checkm_data
[2024-01-24 12:31:44,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:44,459] [INFO] Task started: CheckM
[2024-01-24 12:31:44,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023035295.1_ASM2303529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023035295.1_ASM2303529v1_genomic.fna/checkm_input GCF_023035295.1_ASM2303529v1_genomic.fna/checkm_result
[2024-01-24 12:32:01,284] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:01,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,304] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:01,304] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:01,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023035295.1_ASM2303529v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:01,305] [INFO] Task started: Blastn
[2024-01-24 12:32:01,305] [INFO] Running command: blastn -query GCF_023035295.1_ASM2303529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d612fbc-e5c7-4789-b514-619587fd728e/dqc_reference/reference_markers_gtdb.fasta -out GCF_023035295.1_ASM2303529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:02,036] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:02,040] [INFO] Selected 5 target genomes.
[2024-01-24 12:32:02,040] [INFO] Target genome list was writen to GCF_023035295.1_ASM2303529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:02,045] [INFO] Task started: fastANI
[2024-01-24 12:32:02,045] [INFO] Running command: fastANI --query /var/lib/cwl/stga4224b22-eb85-43b3-9d51-76cf45170394/GCF_023035295.1_ASM2303529v1_genomic.fna.gz --refList GCF_023035295.1_ASM2303529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023035295.1_ASM2303529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:04,565] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,571] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:04,571] [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_000568755.1	s__Borrelia coriaceae	99.849	513	583	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.88	99.88	0.96	0.96	2	conclusive
GCF_000012085.2	s__Borrelia turicatae	87.4977	357	583	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	97.95	97.47	0.93	0.89	4	-
GCF_001660005.1	s__Borrelia hermsii	86.7565	375	583	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	98.15	95.65	0.97	0.94	7	-
GCF_001936255.1	s__Borrelia anserina	85.6284	305	583	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000445425.4	s__Borrelia miyamotoi	84.7954	298	583	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	97.85	96.70	1.00	0.96	22	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,573] [INFO] GTDB search result was written to GCF_023035295.1_ASM2303529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:04,573] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:04,576] [INFO] DFAST_QC result json was written to GCF_023035295.1_ASM2303529v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:04,576] [INFO] DFAST_QC completed!
[2024-01-24 12:32:04,576] [INFO] Total running time: 0h0m31s