[2024-01-24 14:23:04,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,251] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,251] [INFO] DQC Reference Directory: /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference
[2024-01-24 14:23:05,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:05,578] [INFO] Task started: Prodigal
[2024-01-24 14:23:05,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg371edbcd-cc1e-4c7a-baf0-30c7112eaf41/GCF_000421665.1_ASM42166v1_genomic.fna.gz | prodigal -d GCF_000421665.1_ASM42166v1_genomic.fna/cds.fna -a GCF_000421665.1_ASM42166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:09,850] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:09,850] [INFO] Task started: HMMsearch
[2024-01-24 14:23:09,850] [INFO] Running command: hmmsearch --tblout GCF_000421665.1_ASM42166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/reference_markers.hmm GCF_000421665.1_ASM42166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:10,074] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:10,075] [INFO] Found 6/6 markers.
[2024-01-24 14:23:10,101] [INFO] Query marker FASTA was written to GCF_000421665.1_ASM42166v1_genomic.fna/markers.fasta
[2024-01-24 14:23:10,101] [INFO] Task started: Blastn
[2024-01-24 14:23:10,101] [INFO] Running command: blastn -query GCF_000421665.1_ASM42166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/reference_markers.fasta -out GCF_000421665.1_ASM42166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:10,719] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:10,723] [INFO] Selected 26 target genomes.
[2024-01-24 14:23:10,723] [INFO] Target genome list was writen to GCF_000421665.1_ASM42166v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:10,747] [INFO] Task started: fastANI
[2024-01-24 14:23:10,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg371edbcd-cc1e-4c7a-baf0-30c7112eaf41/GCF_000421665.1_ASM42166v1_genomic.fna.gz --refList GCF_000421665.1_ASM42166v1_genomic.fna/target_genomes.txt --output GCF_000421665.1_ASM42166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:19,923] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:19,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:19,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:19,928] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:19,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:19,929] [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
Bavariicoccus seileri	strain=DSM 19936	GCA_000421665.1	549685	549685	type	True	100.0	683	688	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:23:19,930] [INFO] DFAST Taxonomy check result was written to GCF_000421665.1_ASM42166v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:19,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:19,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:19,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/checkm_data
[2024-01-24 14:23:19,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:19,961] [INFO] Task started: CheckM
[2024-01-24 14:23:19,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421665.1_ASM42166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421665.1_ASM42166v1_genomic.fna/checkm_input GCF_000421665.1_ASM42166v1_genomic.fna/checkm_result
[2024-01-24 14:23:41,907] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:41,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:41,977] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:41,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:41,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421665.1_ASM42166v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:41,979] [INFO] Task started: Blastn
[2024-01-24 14:23:41,979] [INFO] Running command: blastn -query GCF_000421665.1_ASM42166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbba06edc-8446-40d1-8dd4-aed68581f338/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421665.1_ASM42166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:42,874] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:42,878] [INFO] Selected 24 target genomes.
[2024-01-24 14:23:42,878] [INFO] Target genome list was writen to GCF_000421665.1_ASM42166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:42,892] [INFO] Task started: fastANI
[2024-01-24 14:23:42,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg371edbcd-cc1e-4c7a-baf0-30c7112eaf41/GCF_000421665.1_ASM42166v1_genomic.fna.gz --refList GCF_000421665.1_ASM42166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421665.1_ASM42166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:52,217] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:52,220] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:52,221] [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_000421665.1	s__Bavariicoccus seileri	100.0	683	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Bavariicoccus	95.0	98.80	97.61	0.89	0.83	3	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,222] [INFO] GTDB search result was written to GCF_000421665.1_ASM42166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:52,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:52,226] [INFO] DFAST_QC result json was written to GCF_000421665.1_ASM42166v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:52,226] [INFO] DFAST_QC completed!
[2024-01-24 14:23:52,226] [INFO] Total running time: 0h0m48s