[2024-01-24 12:15:03,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference
[2024-01-24 12:15:04,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:04,736] [INFO] Task started: Prodigal
[2024-01-24 12:15:04,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg99397cfc-31fe-4226-b8a3-b4586978640c/GCF_004339245.1_ASM433924v1_genomic.fna.gz | prodigal -d GCF_004339245.1_ASM433924v1_genomic.fna/cds.fna -a GCF_004339245.1_ASM433924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:12,168] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:12,168] [INFO] Task started: HMMsearch
[2024-01-24 12:15:12,169] [INFO] Running command: hmmsearch --tblout GCF_004339245.1_ASM433924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/reference_markers.hmm GCF_004339245.1_ASM433924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:12,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:12,434] [INFO] Found 6/6 markers.
[2024-01-24 12:15:12,466] [INFO] Query marker FASTA was written to GCF_004339245.1_ASM433924v1_genomic.fna/markers.fasta
[2024-01-24 12:15:12,466] [INFO] Task started: Blastn
[2024-01-24 12:15:12,466] [INFO] Running command: blastn -query GCF_004339245.1_ASM433924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/reference_markers.fasta -out GCF_004339245.1_ASM433924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:13,052] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:13,056] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:13,056] [INFO] Target genome list was writen to GCF_004339245.1_ASM433924v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:13,064] [INFO] Task started: fastANI
[2024-01-24 12:15:13,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg99397cfc-31fe-4226-b8a3-b4586978640c/GCF_004339245.1_ASM433924v1_genomic.fna.gz --refList GCF_004339245.1_ASM433924v1_genomic.fna/target_genomes.txt --output GCF_004339245.1_ASM433924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:24,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:24,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:24,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:24,203] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:24,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:24,203] [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
Seleniivibrio woodruffii	strain=DSM 24984	GCA_004339245.1	1078050	1078050	type	True	100.0	964	964	95	conclusive
Seleniivibrio woodruffii	strain=S4	GCA_007827295.1	1078050	1078050	type	True	99.9977	964	964	95	conclusive
Denitrovibrio acetiphilus	strain=DSM 12809	GCA_000025725.1	118000	118000	type	True	77.0495	77	964	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:24,205] [INFO] DFAST Taxonomy check result was written to GCF_004339245.1_ASM433924v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:24,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:24,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:24,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/checkm_data
[2024-01-24 12:15:24,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:24,240] [INFO] Task started: CheckM
[2024-01-24 12:15:24,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339245.1_ASM433924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339245.1_ASM433924v1_genomic.fna/checkm_input GCF_004339245.1_ASM433924v1_genomic.fna/checkm_result
[2024-01-24 12:15:52,184] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:52,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:52,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:52,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339245.1_ASM433924v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:52,209] [INFO] Task started: Blastn
[2024-01-24 12:15:52,210] [INFO] Running command: blastn -query GCF_004339245.1_ASM433924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg945af9ef-8d89-46bf-9d2e-93b47fb42fe3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339245.1_ASM433924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:53,025] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:53,030] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:53,030] [INFO] Target genome list was writen to GCF_004339245.1_ASM433924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:53,044] [INFO] Task started: fastANI
[2024-01-24 12:15:53,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg99397cfc-31fe-4226-b8a3-b4586978640c/GCF_004339245.1_ASM433924v1_genomic.fna.gz --refList GCF_004339245.1_ASM433924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339245.1_ASM433924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:03,733] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:03,741] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:03,741] [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_004339245.1	s__Seleniivibrio woodruffii	100.0	964	964	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002452405.1	s__Seleniivibrio sp002452405	80.3941	559	964	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452335.1	s__Seleniivibrio sp002452335	78.0882	315	964	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025725.1	s__Denitrovibrio acetiphilus	77.0495	77	964	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Denitrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:03,743] [INFO] GTDB search result was written to GCF_004339245.1_ASM433924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:03,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:03,750] [INFO] DFAST_QC result json was written to GCF_004339245.1_ASM433924v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:03,750] [INFO] DFAST_QC completed!
[2024-01-24 12:16:03,750] [INFO] Total running time: 0h1m0s