[2024-01-25 20:22:35,467] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:35,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:35,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference
[2024-01-25 20:22:36,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:36,584] [INFO] Task started: Prodigal
[2024-01-25 20:22:36,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a7d81b6-a32c-457e-800c-395aea96d4fd/GCF_032597935.1_ASM3259793v1_genomic.fna.gz | prodigal -d GCF_032597935.1_ASM3259793v1_genomic.fna/cds.fna -a GCF_032597935.1_ASM3259793v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:38,107] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:38,108] [INFO] Task started: HMMsearch
[2024-01-25 20:22:38,108] [INFO] Running command: hmmsearch --tblout GCF_032597935.1_ASM3259793v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/reference_markers.hmm GCF_032597935.1_ASM3259793v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:38,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:38,274] [INFO] Found 6/6 markers.
[2024-01-25 20:22:38,284] [INFO] Query marker FASTA was written to GCF_032597935.1_ASM3259793v1_genomic.fna/markers.fasta
[2024-01-25 20:22:38,285] [INFO] Task started: Blastn
[2024-01-25 20:22:38,285] [INFO] Running command: blastn -query GCF_032597935.1_ASM3259793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/reference_markers.fasta -out GCF_032597935.1_ASM3259793v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:38,845] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:38,848] [INFO] Selected 8 target genomes.
[2024-01-25 20:22:38,848] [INFO] Target genome list was writen to GCF_032597935.1_ASM3259793v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:38,860] [INFO] Task started: fastANI
[2024-01-25 20:22:38,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a7d81b6-a32c-457e-800c-395aea96d4fd/GCF_032597935.1_ASM3259793v1_genomic.fna.gz --refList GCF_032597935.1_ASM3259793v1_genomic.fna/target_genomes.txt --output GCF_032597935.1_ASM3259793v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:40,961] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:40,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:40,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:40,968] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:40,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:40,969] [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 californiensis	strain=DSM 17989	GCA_014205885.1	373543	373543	type	True	99.9971	329	332	95	conclusive
Borreliella bissettiae	strain=DN127	GCA_000222305.1	64897	64897	type	True	94.9669	327	332	95	below_threshold
Borreliella lanei	strain=DSM 17992	GCA_014205895.1	373540	373540	type	True	94.4595	326	332	95	below_threshold
Borreliella burgdorferi	strain=B31_NRZ	GCA_002151505.1	139	139	type	True	94.3198	326	332	95	below_threshold
Borreliella burgdorferi	strain=B31	GCA_000008685.2	139	139	type	True	94.3155	323	332	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	94.2691	328	332	95	below_threshold
Borreliella finlandensis	strain=SV1	GCA_000181875.2	498741	498741	type	True	94.2379	325	332	95	below_threshold
Borreliella mayonii	strain=MN14-1420	GCA_001945665.1	1674146	1674146	type	True	93.8606	328	332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:40,970] [INFO] DFAST Taxonomy check result was written to GCF_032597935.1_ASM3259793v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:40,971] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:40,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:40,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/checkm_data
[2024-01-25 20:22:40,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:40,985] [INFO] Task started: CheckM
[2024-01-25 20:22:40,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032597935.1_ASM3259793v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032597935.1_ASM3259793v1_genomic.fna/checkm_input GCF_032597935.1_ASM3259793v1_genomic.fna/checkm_result
[2024-01-25 20:22:52,583] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:52,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:52,600] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:52,600] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:52,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032597935.1_ASM3259793v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:52,600] [INFO] Task started: Blastn
[2024-01-25 20:22:52,600] [INFO] Running command: blastn -query GCF_032597935.1_ASM3259793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c57d10-5a33-46bb-b3de-105d0d9a846b/dqc_reference/reference_markers_gtdb.fasta -out GCF_032597935.1_ASM3259793v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:53,482] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:53,484] [INFO] Selected 7 target genomes.
[2024-01-25 20:22:53,484] [INFO] Target genome list was writen to GCF_032597935.1_ASM3259793v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:53,488] [INFO] Task started: fastANI
[2024-01-25 20:22:53,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a7d81b6-a32c-457e-800c-395aea96d4fd/GCF_032597935.1_ASM3259793v1_genomic.fna.gz --refList GCF_032597935.1_ASM3259793v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032597935.1_ASM3259793v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:55,460] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:55,466] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:55,466] [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_014205885.1	s__Borreliella californiensis	99.9971	329	332	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000222305.1	s__Borreliella bissettiae	94.9669	327	332	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	94.4786	325	332	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	94.3155	323	332	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	-
GCF_000181875.2	s__Borreliella finlandensis	94.2379	325	332	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	N/A	N/A	N/A	N/A	1	-
GCF_001945665.1	s__Borreliella mayonii	93.8606	328	332	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014202295.1	s__Borreliella afzelii	91.865	321	332	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.29	99.08	0.96	0.92	10	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:55,467] [INFO] GTDB search result was written to GCF_032597935.1_ASM3259793v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:55,468] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:55,470] [INFO] DFAST_QC result json was written to GCF_032597935.1_ASM3259793v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:55,470] [INFO] DFAST_QC completed!
[2024-01-25 20:22:55,470] [INFO] Total running time: 0h0m20s