[2024-01-24 14:02:49,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:49,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:49,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference
[2024-01-24 14:02:50,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:50,931] [INFO] Task started: Prodigal
[2024-01-24 14:02:50,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg2939979d-02f6-4605-b401-2cefbe8a8bff/GCF_000621365.1_ASM62136v1_genomic.fna.gz | prodigal -d GCF_000621365.1_ASM62136v1_genomic.fna/cds.fna -a GCF_000621365.1_ASM62136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:02:58,537] [INFO] Task succeeded: Prodigal
[2024-01-24 14:02:58,538] [INFO] Task started: HMMsearch
[2024-01-24 14:02:58,538] [INFO] Running command: hmmsearch --tblout GCF_000621365.1_ASM62136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/reference_markers.hmm GCF_000621365.1_ASM62136v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:02:58,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:02:58,807] [INFO] Found 6/6 markers.
[2024-01-24 14:02:58,836] [INFO] Query marker FASTA was written to GCF_000621365.1_ASM62136v1_genomic.fna/markers.fasta
[2024-01-24 14:02:58,837] [INFO] Task started: Blastn
[2024-01-24 14:02:58,837] [INFO] Running command: blastn -query GCF_000621365.1_ASM62136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/reference_markers.fasta -out GCF_000621365.1_ASM62136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:02:59,544] [INFO] Task succeeded: Blastn
[2024-01-24 14:02:59,549] [INFO] Selected 10 target genomes.
[2024-01-24 14:02:59,550] [INFO] Target genome list was writen to GCF_000621365.1_ASM62136v1_genomic.fna/target_genomes.txt
[2024-01-24 14:02:59,559] [INFO] Task started: fastANI
[2024-01-24 14:02:59,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg2939979d-02f6-4605-b401-2cefbe8a8bff/GCF_000621365.1_ASM62136v1_genomic.fna.gz --refList GCF_000621365.1_ASM62136v1_genomic.fna/target_genomes.txt --output GCF_000621365.1_ASM62136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:06,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:06,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:06,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:06,770] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:03:06,771] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:06,771] [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
Legionella geestiana	strain=DSM 21217	GCA_000621365.1	45065	45065	type	True	100.0	808	812	95	conclusive
Legionella geestiana	strain=NCTC12373	GCA_900452375.1	45065	45065	type	True	99.9844	810	812	95	conclusive
Legionella geestiana	strain=1308	GCA_004571195.1	45065	45065	type	True	99.9814	811	812	95	conclusive
Legionella geestiana	strain=1308	GCA_900639805.1	45065	45065	type	True	99.9747	797	812	95	conclusive
Legionella geestiana	strain=ATCC 49504	GCA_001467645.1	45065	45065	type	True	99.9516	764	812	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:03:06,772] [INFO] DFAST Taxonomy check result was written to GCF_000621365.1_ASM62136v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:06,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:06,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:06,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/checkm_data
[2024-01-24 14:03:06,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:06,801] [INFO] Task started: CheckM
[2024-01-24 14:03:06,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621365.1_ASM62136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621365.1_ASM62136v1_genomic.fna/checkm_input GCF_000621365.1_ASM62136v1_genomic.fna/checkm_result
[2024-01-24 14:03:34,265] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:34,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:34,285] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:34,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:34,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621365.1_ASM62136v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:34,286] [INFO] Task started: Blastn
[2024-01-24 14:03:34,286] [INFO] Running command: blastn -query GCF_000621365.1_ASM62136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb2c709a-550a-4dcf-aa15-abe764df5ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621365.1_ASM62136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:35,371] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:35,374] [INFO] Selected 29 target genomes.
[2024-01-24 14:03:35,374] [INFO] Target genome list was writen to GCF_000621365.1_ASM62136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:35,418] [INFO] Task started: fastANI
[2024-01-24 14:03:35,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg2939979d-02f6-4605-b401-2cefbe8a8bff/GCF_000621365.1_ASM62136v1_genomic.fna.gz --refList GCF_000621365.1_ASM62136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621365.1_ASM62136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:49,713] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:49,716] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:49,716] [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_004571195.1	s__Legionella_B geestiana	99.9814	811	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_B	95.0	99.84	99.28	0.98	0.92	6	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:03:49,718] [INFO] GTDB search result was written to GCF_000621365.1_ASM62136v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:49,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:49,721] [INFO] DFAST_QC result json was written to GCF_000621365.1_ASM62136v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:49,721] [INFO] DFAST_QC completed!
[2024-01-24 14:03:49,721] [INFO] Total running time: 0h1m0s