[2024-01-24 13:32:42,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference
[2024-01-24 13:32:43,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,770] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgac281edf-ca0c-415e-b4f2-2e288a810675/GCF_020564625.1_ASM2056462v1_genomic.fna.gz | prodigal -d GCF_020564625.1_ASM2056462v1_genomic.fna/cds.fna -a GCF_020564625.1_ASM2056462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:53,104] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:53,105] [INFO] Task started: HMMsearch
[2024-01-24 13:32:53,105] [INFO] Running command: hmmsearch --tblout GCF_020564625.1_ASM2056462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/reference_markers.hmm GCF_020564625.1_ASM2056462v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:53,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:53,418] [INFO] Found 6/6 markers.
[2024-01-24 13:32:53,455] [INFO] Query marker FASTA was written to GCF_020564625.1_ASM2056462v1_genomic.fna/markers.fasta
[2024-01-24 13:32:53,456] [INFO] Task started: Blastn
[2024-01-24 13:32:53,456] [INFO] Running command: blastn -query GCF_020564625.1_ASM2056462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/reference_markers.fasta -out GCF_020564625.1_ASM2056462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:54,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:54,168] [INFO] Selected 26 target genomes.
[2024-01-24 13:32:54,169] [INFO] Target genome list was writen to GCF_020564625.1_ASM2056462v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:54,178] [INFO] Task started: fastANI
[2024-01-24 13:32:54,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgac281edf-ca0c-415e-b4f2-2e288a810675/GCF_020564625.1_ASM2056462v1_genomic.fna.gz --refList GCF_020564625.1_ASM2056462v1_genomic.fna/target_genomes.txt --output GCF_020564625.1_ASM2056462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:13,737] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:13,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:13,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:13,742] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:13,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:13,743] [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
Leeia oryzae	strain=DSM 17879	GCA_000376945.1	356662	356662	type	True	78.0051	204	1243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:13,744] [INFO] DFAST Taxonomy check result was written to GCF_020564625.1_ASM2056462v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:13,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:13,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:13,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/checkm_data
[2024-01-24 13:33:13,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:13,789] [INFO] Task started: CheckM
[2024-01-24 13:33:13,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020564625.1_ASM2056462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020564625.1_ASM2056462v1_genomic.fna/checkm_input GCF_020564625.1_ASM2056462v1_genomic.fna/checkm_result
[2024-01-24 13:33:45,610] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:45,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:45,629] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:45,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:45,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020564625.1_ASM2056462v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:45,630] [INFO] Task started: Blastn
[2024-01-24 13:33:45,630] [INFO] Running command: blastn -query GCF_020564625.1_ASM2056462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22302bc5-60fa-47ec-bc3e-8b2159c8e9f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_020564625.1_ASM2056462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:46,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:46,614] [INFO] Selected 34 target genomes.
[2024-01-24 13:33:46,614] [INFO] Target genome list was writen to GCF_020564625.1_ASM2056462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:46,680] [INFO] Task started: fastANI
[2024-01-24 13:33:46,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgac281edf-ca0c-415e-b4f2-2e288a810675/GCF_020564625.1_ASM2056462v1_genomic.fna.gz --refList GCF_020564625.1_ASM2056462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020564625.1_ASM2056462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:06,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:06,300] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:06,301] [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_000376945.1	s__Leeia oryzae	77.9829	206	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:06,302] [INFO] GTDB search result was written to GCF_020564625.1_ASM2056462v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:06,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:06,305] [INFO] DFAST_QC result json was written to GCF_020564625.1_ASM2056462v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:06,305] [INFO] DFAST_QC completed!
[2024-01-24 13:34:06,306] [INFO] Total running time: 0h1m24s