[2024-01-25 19:02:20,687] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference
[2024-01-25 19:02:21,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,810] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b3fc111-03bd-4e64-91ef-dcfd0a66c779/GCF_000008685.2_ASM868v2_genomic.fna.gz | prodigal -d GCF_000008685.2_ASM868v2_genomic.fna/cds.fna -a GCF_000008685.2_ASM868v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:23,993] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:23,994] [INFO] Task started: HMMsearch
[2024-01-25 19:02:23,994] [INFO] Running command: hmmsearch --tblout GCF_000008685.2_ASM868v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/reference_markers.hmm GCF_000008685.2_ASM868v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:24,186] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:24,187] [INFO] Found 6/6 markers.
[2024-01-25 19:02:24,206] [INFO] Query marker FASTA was written to GCF_000008685.2_ASM868v2_genomic.fna/markers.fasta
[2024-01-25 19:02:24,206] [INFO] Task started: Blastn
[2024-01-25 19:02:24,206] [INFO] Running command: blastn -query GCF_000008685.2_ASM868v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/reference_markers.fasta -out GCF_000008685.2_ASM868v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:24,780] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:24,784] [INFO] Selected 6 target genomes.
[2024-01-25 19:02:24,785] [INFO] Target genome list was writen to GCF_000008685.2_ASM868v2_genomic.fna/target_genomes.txt
[2024-01-25 19:02:24,789] [INFO] Task started: fastANI
[2024-01-25 19:02:24,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3fc111-03bd-4e64-91ef-dcfd0a66c779/GCF_000008685.2_ASM868v2_genomic.fna.gz --refList GCF_000008685.2_ASM868v2_genomic.fna/target_genomes.txt --output GCF_000008685.2_ASM868v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:27,810] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:27,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:27,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:27,816] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:02:27,816] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:02:27,817] [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 burgdorferi	strain=B31	GCA_000008685.2	139	139	type	True	100.0	495	497	95	inconclusive
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	99.8993	431	497	95	inconclusive
Borreliella burgdorferi	strain=B31_NRZ	GCA_002151505.1	139	139	type	True	99.8222	431	497	95	inconclusive
Borreliella finlandensis	strain=SV1	GCA_000181875.2	498741	498741	type	True	96.5708	371	497	95	inconclusive
Borreliella lanei	strain=DSM 17992	GCA_014205895.1	373540	373540	type	True	94.4522	358	497	95	below_threshold
Borreliella bissettiae	strain=DN127	GCA_000222305.1	64897	64897	type	True	93.6318	398	497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:27,818] [INFO] DFAST Taxonomy check result was written to GCF_000008685.2_ASM868v2_genomic.fna/tc_result.tsv
[2024-01-25 19:02:27,818] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:27,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:27,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/checkm_data
[2024-01-25 19:02:27,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:27,837] [INFO] Task started: CheckM
[2024-01-25 19:02:27,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000008685.2_ASM868v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000008685.2_ASM868v2_genomic.fna/checkm_input GCF_000008685.2_ASM868v2_genomic.fna/checkm_result
[2024-01-25 19:02:41,300] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:41,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:41,313] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:41,313] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:41,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000008685.2_ASM868v2_genomic.fna/markers.fasta)
[2024-01-25 19:02:41,314] [INFO] Task started: Blastn
[2024-01-25 19:02:41,314] [INFO] Running command: blastn -query GCF_000008685.2_ASM868v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e15bbd-6b63-49a0-a76c-f296e93b60f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000008685.2_ASM868v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:42,234] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:42,236] [INFO] Selected 7 target genomes.
[2024-01-25 19:02:42,236] [INFO] Target genome list was writen to GCF_000008685.2_ASM868v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:42,242] [INFO] Task started: fastANI
[2024-01-25 19:02:42,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3fc111-03bd-4e64-91ef-dcfd0a66c779/GCF_000008685.2_ASM868v2_genomic.fna.gz --refList GCF_000008685.2_ASM868v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000008685.2_ASM868v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:45,458] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:45,463] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:45,463] [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_000008685.2	s__Borreliella burgdorferi	100.0	497	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	conclusive
GCF_000181875.2	s__Borreliella finlandensis	96.6301	370	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	N/A	N/A	N/A	N/A	1	-
GCF_014205895.1	s__Borreliella lanei	94.4967	357	497	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	93.6439	384	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000222305.1	s__Borreliella bissettiae	93.6223	399	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205885.1	s__Borreliella californiensis	93.3523	373	497	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 19:02:45,464] [INFO] GTDB search result was written to GCF_000008685.2_ASM868v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:45,465] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:45,467] [INFO] DFAST_QC result json was written to GCF_000008685.2_ASM868v2_genomic.fna/dqc_result.json
[2024-01-25 19:02:45,467] [INFO] DFAST_QC completed!
[2024-01-25 19:02:45,467] [INFO] Total running time: 0h0m25s