[2024-01-24 12:44:09,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:09,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:09,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference
[2024-01-24 12:44:11,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,114] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgac7a8f84-c2c8-4c4d-b7fd-747eac4bfb13/GCF_002892535.1_ASM289253v1_genomic.fna.gz | prodigal -d GCF_002892535.1_ASM289253v1_genomic.fna/cds.fna -a GCF_002892535.1_ASM289253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:16,539] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:16,539] [INFO] Task started: HMMsearch
[2024-01-24 12:44:16,539] [INFO] Running command: hmmsearch --tblout GCF_002892535.1_ASM289253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/reference_markers.hmm GCF_002892535.1_ASM289253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:16,807] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:16,809] [INFO] Found 6/6 markers.
[2024-01-24 12:44:16,836] [INFO] Query marker FASTA was written to GCF_002892535.1_ASM289253v1_genomic.fna/markers.fasta
[2024-01-24 12:44:16,836] [INFO] Task started: Blastn
[2024-01-24 12:44:16,836] [INFO] Running command: blastn -query GCF_002892535.1_ASM289253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/reference_markers.fasta -out GCF_002892535.1_ASM289253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:17,438] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:17,442] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:17,442] [INFO] Target genome list was writen to GCF_002892535.1_ASM289253v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:17,488] [INFO] Task started: fastANI
[2024-01-24 12:44:17,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7a8f84-c2c8-4c4d-b7fd-747eac4bfb13/GCF_002892535.1_ASM289253v1_genomic.fna.gz --refList GCF_002892535.1_ASM289253v1_genomic.fna/target_genomes.txt --output GCF_002892535.1_ASM289253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:25,544] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:25,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:25,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:25,549] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:25,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:25,549] [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
Aquella oligotrophica	strain=DSM 100970	GCA_002892535.1	2067065	2067065	type	True	100.0	940	940	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:44:25,552] [INFO] DFAST Taxonomy check result was written to GCF_002892535.1_ASM289253v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:25,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:25,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:25,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/checkm_data
[2024-01-24 12:44:25,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:25,591] [INFO] Task started: CheckM
[2024-01-24 12:44:25,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002892535.1_ASM289253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002892535.1_ASM289253v1_genomic.fna/checkm_input GCF_002892535.1_ASM289253v1_genomic.fna/checkm_result
[2024-01-24 12:44:49,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:49,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:49,554] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:49,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:49,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002892535.1_ASM289253v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:49,555] [INFO] Task started: Blastn
[2024-01-24 12:44:49,555] [INFO] Running command: blastn -query GCF_002892535.1_ASM289253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6149cafa-ecec-4cab-aa51-fe5791c9f57a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002892535.1_ASM289253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:50,410] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:50,414] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:50,414] [INFO] Target genome list was writen to GCF_002892535.1_ASM289253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:50,448] [INFO] Task started: fastANI
[2024-01-24 12:44:50,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7a8f84-c2c8-4c4d-b7fd-747eac4bfb13/GCF_002892535.1_ASM289253v1_genomic.fna.gz --refList GCF_002892535.1_ASM289253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002892535.1_ASM289253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:56,566] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:56,573] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:56,573] [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
GCA_002892535.1	s__UBA11063 sp002892535	100.0	940	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008017155.1	s__UBA11063 sp008017155	89.6009	488	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963245.1	s__UBA11063 sp003963245	77.4674	143	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962895.1	s__UBA11063 sp003962895	77.027	63	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008017145.1	s__UBA11063 sp008017145	76.8477	120	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962985.1	s__UBA11063 sp003962985	76.6352	97	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA11063;g__UBA11063	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:56,575] [INFO] GTDB search result was written to GCF_002892535.1_ASM289253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:56,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:56,578] [INFO] DFAST_QC result json was written to GCF_002892535.1_ASM289253v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:56,579] [INFO] DFAST_QC completed!
[2024-01-24 12:44:56,579] [INFO] Total running time: 0h0m47s