[2024-01-24 12:21:36,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,164] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference
[2024-01-24 12:21:37,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,423] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bc29af3-b3e6-4d7e-b2ed-4d50fc6bfa15/GCF_001263335.1_ASM126333v1_genomic.fna.gz | prodigal -d GCF_001263335.1_ASM126333v1_genomic.fna/cds.fna -a GCF_001263335.1_ASM126333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:41,083] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:41,084] [INFO] Task started: HMMsearch
[2024-01-24 12:21:41,084] [INFO] Running command: hmmsearch --tblout GCF_001263335.1_ASM126333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/reference_markers.hmm GCF_001263335.1_ASM126333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:41,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:41,302] [INFO] Found 6/6 markers.
[2024-01-24 12:21:41,322] [INFO] Query marker FASTA was written to GCF_001263335.1_ASM126333v1_genomic.fna/markers.fasta
[2024-01-24 12:21:41,323] [INFO] Task started: Blastn
[2024-01-24 12:21:41,323] [INFO] Running command: blastn -query GCF_001263335.1_ASM126333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/reference_markers.fasta -out GCF_001263335.1_ASM126333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:41,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:41,964] [INFO] Selected 27 target genomes.
[2024-01-24 12:21:41,965] [INFO] Target genome list was writen to GCF_001263335.1_ASM126333v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:42,283] [INFO] Task started: fastANI
[2024-01-24 12:21:42,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc29af3-b3e6-4d7e-b2ed-4d50fc6bfa15/GCF_001263335.1_ASM126333v1_genomic.fna.gz --refList GCF_001263335.1_ASM126333v1_genomic.fna/target_genomes.txt --output GCF_001263335.1_ASM126333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:54,497] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:54,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:54,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:54,506] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:21:54,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:54,507] [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
Dichelobacter nodosus	strain=VPI 2340	GCA_001263335.1	870	870	type	True	100.0	467	470	95	conclusive
Suttonella indologenes	strain=NCTC10717	GCA_900460215.1	13276	13276	type	True	77.9759	55	470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:54,509] [INFO] DFAST Taxonomy check result was written to GCF_001263335.1_ASM126333v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:54,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:54,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:54,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/checkm_data
[2024-01-24 12:21:54,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:54,533] [INFO] Task started: CheckM
[2024-01-24 12:21:54,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001263335.1_ASM126333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001263335.1_ASM126333v1_genomic.fna/checkm_input GCF_001263335.1_ASM126333v1_genomic.fna/checkm_result
[2024-01-24 12:22:12,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:12,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:12,455] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:12,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:12,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001263335.1_ASM126333v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:12,457] [INFO] Task started: Blastn
[2024-01-24 12:22:12,457] [INFO] Running command: blastn -query GCF_001263335.1_ASM126333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd407218-7b14-4ae6-ade1-b738c4419023/dqc_reference/reference_markers_gtdb.fasta -out GCF_001263335.1_ASM126333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:13,484] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:13,490] [INFO] Selected 29 target genomes.
[2024-01-24 12:22:13,490] [INFO] Target genome list was writen to GCF_001263335.1_ASM126333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:13,576] [INFO] Task started: fastANI
[2024-01-24 12:22:13,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bc29af3-b3e6-4d7e-b2ed-4d50fc6bfa15/GCF_001263335.1_ASM126333v1_genomic.fna.gz --refList GCF_001263335.1_ASM126333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001263335.1_ASM126333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:26,364] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,370] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:26,371] [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_001263335.1	s__Dichelobacter nodosus	100.0	467	470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Cardiobacteriaceae;g__Dichelobacter	95.0	99.72	99.69	0.95	0.93	4	conclusive
GCF_900460215.1	s__Suttonella indologenes	77.9759	55	470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Cardiobacteriaceae;g__Suttonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,373] [INFO] GTDB search result was written to GCF_001263335.1_ASM126333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:26,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:26,378] [INFO] DFAST_QC result json was written to GCF_001263335.1_ASM126333v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:26,378] [INFO] DFAST_QC completed!
[2024-01-24 12:22:26,378] [INFO] Total running time: 0h0m50s