[2024-01-24 13:17:30,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:30,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:30,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference
[2024-01-24 13:17:31,406] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:31,407] [INFO] Task started: Prodigal
[2024-01-24 13:17:31,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg759ffb82-e441-4c92-b26e-ef8bb2bf2a10/GCF_000012065.2_ASM1206v2_genomic.fna.gz | prodigal -d GCF_000012065.2_ASM1206v2_genomic.fna/cds.fna -a GCF_000012065.2_ASM1206v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,252] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,252] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,252] [INFO] Running command: hmmsearch --tblout GCF_000012065.2_ASM1206v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/reference_markers.hmm GCF_000012065.2_ASM1206v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,454] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,473] [INFO] Query marker FASTA was written to GCF_000012065.2_ASM1206v2_genomic.fna/markers.fasta
[2024-01-24 13:17:33,474] [INFO] Task started: Blastn
[2024-01-24 13:17:33,474] [INFO] Running command: blastn -query GCF_000012065.2_ASM1206v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/reference_markers.fasta -out GCF_000012065.2_ASM1206v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,145] [INFO] Selected 6 target genomes.
[2024-01-24 13:17:34,146] [INFO] Target genome list was writen to GCF_000012065.2_ASM1206v2_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,168] [INFO] Task started: fastANI
[2024-01-24 13:17:34,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg759ffb82-e441-4c92-b26e-ef8bb2bf2a10/GCF_000012065.2_ASM1206v2_genomic.fna.gz --refList GCF_000012065.2_ASM1206v2_genomic.fna/target_genomes.txt --output GCF_000012065.2_ASM1206v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:36,647] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:36,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:36,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:36,659] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:36,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:36,659] [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 hermsii	strain=DAH	GCA_000012065.2	140	140	suspected-type	True	100.0	348	349	95	conclusive
Borrelia hermsii	strain=DAH	GCA_023035675.1	140	140	suspected-type	True	99.9889	349	349	95	conclusive
Borrelia parkeri	strain=SLO	GCA_000568735.2	141	141	reftype	True	90.6606	297	349	95	below_threshold
Borrelia turicatae	strain=91E135	GCA_000012085.2	142	142	reftype	True	89.9942	328	349	95	below_threshold
Borrelia puertoricensis	strain=SUM	GCA_023035875.1	2756107	2756107	type	True	89.1844	331	349	95	below_threshold
Borrelia coriaceae	strain=Co53	GCA_023035295.1	144	144	type	True	87.5713	326	349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:36,661] [INFO] DFAST Taxonomy check result was written to GCF_000012065.2_ASM1206v2_genomic.fna/tc_result.tsv
[2024-01-24 13:17:36,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:36,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:36,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/checkm_data
[2024-01-24 13:17:36,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:36,683] [INFO] Task started: CheckM
[2024-01-24 13:17:36,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012065.2_ASM1206v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012065.2_ASM1206v2_genomic.fna/checkm_input GCF_000012065.2_ASM1206v2_genomic.fna/checkm_result
[2024-01-24 13:17:51,071] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:51,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,094] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:51,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:51,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012065.2_ASM1206v2_genomic.fna/markers.fasta)
[2024-01-24 13:17:51,096] [INFO] Task started: Blastn
[2024-01-24 13:17:51,096] [INFO] Running command: blastn -query GCF_000012065.2_ASM1206v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg85560c0f-dadc-4c96-9530-457ad1dfffdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012065.2_ASM1206v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:52,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:52,147] [INFO] Selected 5 target genomes.
[2024-01-24 13:17:52,148] [INFO] Target genome list was writen to GCF_000012065.2_ASM1206v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:52,152] [INFO] Task started: fastANI
[2024-01-24 13:17:52,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg759ffb82-e441-4c92-b26e-ef8bb2bf2a10/GCF_000012065.2_ASM1206v2_genomic.fna.gz --refList GCF_000012065.2_ASM1206v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000012065.2_ASM1206v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:53,962] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:53,970] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:53,970] [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_001660005.1	s__Borrelia hermsii	99.9806	345	349	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	98.15	95.65	0.97	0.94	7	conclusive
GCF_000012085.2	s__Borrelia turicatae	89.9946	328	349	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	97.95	97.47	0.93	0.89	4	-
GCF_001936255.1	s__Borrelia anserina	87.9526	295	349	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000568755.1	s__Borrelia coriaceae	87.6303	320	349	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.88	99.88	0.96	0.96	2	-
GCF_000445425.4	s__Borrelia miyamotoi	86.6372	298	349	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 13:17:53,972] [INFO] GTDB search result was written to GCF_000012065.2_ASM1206v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:53,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:53,976] [INFO] DFAST_QC result json was written to GCF_000012065.2_ASM1206v2_genomic.fna/dqc_result.json
[2024-01-24 13:17:53,976] [INFO] DFAST_QC completed!
[2024-01-24 13:17:53,977] [INFO] Total running time: 0h0m24s