[2024-01-25 17:52:05,283] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:05,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:05,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference
[2024-01-25 17:52:06,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:06,401] [INFO] Task started: Prodigal
[2024-01-25 17:52:06,401] [INFO] Running command: gunzip -c /var/lib/cwl/stge37decb9-868d-4a15-a719-9dd40a35c87e/GCF_001889065.1_ASM188906v1_genomic.fna.gz | prodigal -d GCF_001889065.1_ASM188906v1_genomic.fna/cds.fna -a GCF_001889065.1_ASM188906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:10,324] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:10,325] [INFO] Task started: HMMsearch
[2024-01-25 17:52:10,325] [INFO] Running command: hmmsearch --tblout GCF_001889065.1_ASM188906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/reference_markers.hmm GCF_001889065.1_ASM188906v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:10,538] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:10,539] [INFO] Found 6/6 markers.
[2024-01-25 17:52:10,563] [INFO] Query marker FASTA was written to GCF_001889065.1_ASM188906v1_genomic.fna/markers.fasta
[2024-01-25 17:52:10,563] [INFO] Task started: Blastn
[2024-01-25 17:52:10,564] [INFO] Running command: blastn -query GCF_001889065.1_ASM188906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/reference_markers.fasta -out GCF_001889065.1_ASM188906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:11,159] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:11,162] [INFO] Selected 21 target genomes.
[2024-01-25 17:52:11,162] [INFO] Target genome list was writen to GCF_001889065.1_ASM188906v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:11,190] [INFO] Task started: fastANI
[2024-01-25 17:52:11,190] [INFO] Running command: fastANI --query /var/lib/cwl/stge37decb9-868d-4a15-a719-9dd40a35c87e/GCF_001889065.1_ASM188906v1_genomic.fna.gz --refList GCF_001889065.1_ASM188906v1_genomic.fna/target_genomes.txt --output GCF_001889065.1_ASM188906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:26,976] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:26,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:26,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:26,981] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:52:26,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:26,982] [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
Suttonella ornithocola	strain=CCUG 49457	GCA_001889065.1	279832	279832	type	True	100.0	685	692	95	conclusive
Suttonella ornithocola	strain=NCTC13337	GCA_900460265.1	279832	279832	type	True	99.977	688	692	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:52:26,983] [INFO] DFAST Taxonomy check result was written to GCF_001889065.1_ASM188906v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:26,984] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:26,984] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:26,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/checkm_data
[2024-01-25 17:52:26,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:27,014] [INFO] Task started: CheckM
[2024-01-25 17:52:27,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001889065.1_ASM188906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001889065.1_ASM188906v1_genomic.fna/checkm_input GCF_001889065.1_ASM188906v1_genomic.fna/checkm_result
[2024-01-25 17:52:44,921] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:44,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:44,942] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:44,942] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:44,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001889065.1_ASM188906v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:44,943] [INFO] Task started: Blastn
[2024-01-25 17:52:44,943] [INFO] Running command: blastn -query GCF_001889065.1_ASM188906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36df2016-0d4b-41e0-8d0a-d9cef6debadb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001889065.1_ASM188906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:45,922] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:45,924] [INFO] Selected 26 target genomes.
[2024-01-25 17:52:45,924] [INFO] Target genome list was writen to GCF_001889065.1_ASM188906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:45,943] [INFO] Task started: fastANI
[2024-01-25 17:52:45,944] [INFO] Running command: fastANI --query /var/lib/cwl/stge37decb9-868d-4a15-a719-9dd40a35c87e/GCF_001889065.1_ASM188906v1_genomic.fna.gz --refList GCF_001889065.1_ASM188906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001889065.1_ASM188906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:59,890] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:59,892] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:59,893] [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_001889065.1	s__Suttonella ornithocola	100.0	685	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Cardiobacteriaceae;g__Suttonella	95.0	99.98	99.98	0.99	0.99	2	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:52:59,894] [INFO] GTDB search result was written to GCF_001889065.1_ASM188906v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:59,895] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:59,897] [INFO] DFAST_QC result json was written to GCF_001889065.1_ASM188906v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:59,897] [INFO] DFAST_QC completed!
[2024-01-25 17:52:59,897] [INFO] Total running time: 0h0m55s