[2024-01-24 13:57:28,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:28,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:28,689] [INFO] DQC Reference Directory: /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference
[2024-01-24 13:57:30,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:30,001] [INFO] Task started: Prodigal
[2024-01-24 13:57:30,001] [INFO] Running command: gunzip -c /var/lib/cwl/stge18276f2-8bd7-475e-9ff2-202f560d2f6d/GCF_032595875.1_ASM3259587v1_genomic.fna.gz | prodigal -d GCF_032595875.1_ASM3259587v1_genomic.fna/cds.fna -a GCF_032595875.1_ASM3259587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:31,732] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:31,733] [INFO] Task started: HMMsearch
[2024-01-24 13:57:31,733] [INFO] Running command: hmmsearch --tblout GCF_032595875.1_ASM3259587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/reference_markers.hmm GCF_032595875.1_ASM3259587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:31,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:31,952] [INFO] Found 6/6 markers.
[2024-01-24 13:57:31,971] [INFO] Query marker FASTA was written to GCF_032595875.1_ASM3259587v1_genomic.fna/markers.fasta
[2024-01-24 13:57:31,972] [INFO] Task started: Blastn
[2024-01-24 13:57:31,972] [INFO] Running command: blastn -query GCF_032595875.1_ASM3259587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/reference_markers.fasta -out GCF_032595875.1_ASM3259587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:32,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:32,689] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:32,690] [INFO] Target genome list was writen to GCF_032595875.1_ASM3259587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:32,695] [INFO] Task started: fastANI
[2024-01-24 13:57:32,695] [INFO] Running command: fastANI --query /var/lib/cwl/stge18276f2-8bd7-475e-9ff2-202f560d2f6d/GCF_032595875.1_ASM3259587v1_genomic.fna.gz --refList GCF_032595875.1_ASM3259587v1_genomic.fna/target_genomes.txt --output GCF_032595875.1_ASM3259587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:34,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:34,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:34,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:34,596] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:34,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:34,596] [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_NRZ	GCA_002151505.1	139	139	type	True	94.1002	325	330	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	94.091	327	330	95	below_threshold
Borreliella finlandensis	strain=SV1	GCA_000181875.2	498741	498741	type	True	94.0584	322	330	95	below_threshold
Borreliella burgdorferi	strain=B31	GCA_000008685.2	139	139	type	True	94.0341	326	330	95	below_threshold
Borreliella lanei	strain=DSM 17992	GCA_014205895.1	373540	373540	type	True	93.9748	325	330	95	below_threshold
Borreliella californiensis	strain=DSM 17989	GCA_014205885.1	373543	373543	type	True	93.2447	322	330	95	below_threshold
Borreliella bissettiae	strain=DN127	GCA_000222305.1	64897	64897	type	True	93.1403	325	330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:34,598] [INFO] DFAST Taxonomy check result was written to GCF_032595875.1_ASM3259587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:34,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:34,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:34,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/checkm_data
[2024-01-24 13:57:34,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:34,611] [INFO] Task started: CheckM
[2024-01-24 13:57:34,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032595875.1_ASM3259587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032595875.1_ASM3259587v1_genomic.fna/checkm_input GCF_032595875.1_ASM3259587v1_genomic.fna/checkm_result
[2024-01-24 13:57:49,045] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:49,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:49,069] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:49,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:49,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032595875.1_ASM3259587v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:49,070] [INFO] Task started: Blastn
[2024-01-24 13:57:49,070] [INFO] Running command: blastn -query GCF_032595875.1_ASM3259587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92c37e4-0326-418c-9521-08b51a0aed52/dqc_reference/reference_markers_gtdb.fasta -out GCF_032595875.1_ASM3259587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:50,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:50,056] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:50,056] [INFO] Target genome list was writen to GCF_032595875.1_ASM3259587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:50,060] [INFO] Task started: fastANI
[2024-01-24 13:57:50,061] [INFO] Running command: fastANI --query /var/lib/cwl/stge18276f2-8bd7-475e-9ff2-202f560d2f6d/GCF_032595875.1_ASM3259587v1_genomic.fna.gz --refList GCF_032595875.1_ASM3259587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032595875.1_ASM3259587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:51,783] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:51,790] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:51,790] [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_000181875.2	s__Borreliella finlandensis	94.0584	322	330	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	N/A	N/A	N/A	N/A	1	-
GCF_000008685.2	s__Borreliella burgdorferi	94.0341	326	330	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	96.6606	99.04	98.60	0.96	0.83	102	-
GCF_014205895.1	s__Borreliella lanei	93.9748	325	330	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	93.2916	322	330	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222305.1	s__Borreliella bissettiae	93.1403	325	330	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	93.0089	328	330	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:51,792] [INFO] GTDB search result was written to GCF_032595875.1_ASM3259587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:51,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:51,799] [INFO] DFAST_QC result json was written to GCF_032595875.1_ASM3259587v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:51,799] [INFO] DFAST_QC completed!
[2024-01-24 13:57:51,800] [INFO] Total running time: 0h0m23s