[2024-01-24 11:05:25,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference
[2024-01-24 11:05:26,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,538] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,538] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb1eb605-550b-466b-9f1f-96031e9e6f60/GCF_003350455.1_ASM335045v1_genomic.fna.gz | prodigal -d GCF_003350455.1_ASM335045v1_genomic.fna/cds.fna -a GCF_003350455.1_ASM335045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:32,735] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:32,736] [INFO] Task started: HMMsearch
[2024-01-24 11:05:32,736] [INFO] Running command: hmmsearch --tblout GCF_003350455.1_ASM335045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/reference_markers.hmm GCF_003350455.1_ASM335045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:32,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:32,980] [INFO] Found 6/6 markers.
[2024-01-24 11:05:33,006] [INFO] Query marker FASTA was written to GCF_003350455.1_ASM335045v1_genomic.fna/markers.fasta
[2024-01-24 11:05:33,007] [INFO] Task started: Blastn
[2024-01-24 11:05:33,007] [INFO] Running command: blastn -query GCF_003350455.1_ASM335045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/reference_markers.fasta -out GCF_003350455.1_ASM335045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:33,679] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:33,682] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:33,683] [INFO] Target genome list was writen to GCF_003350455.1_ASM335045v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:33,708] [INFO] Task started: fastANI
[2024-01-24 11:05:33,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1eb605-550b-466b-9f1f-96031e9e6f60/GCF_003350455.1_ASM335045v1_genomic.fna.gz --refList GCF_003350455.1_ASM335045v1_genomic.fna/target_genomes.txt --output GCF_003350455.1_ASM335045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:45,442] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:45,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:45,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:45,452] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:45,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:45,452] [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
Aquicella lusitana	strain=DSM 16500	GCA_003350455.1	254246	254246	type	True	100.0	805	808	95	conclusive
Aquicella lusitana	strain=SGT-39	GCA_902459475.1	254246	254246	type	True	99.9902	805	808	95	conclusive
Aquicella siphonis	strain=SGT-108	GCA_902459485.1	254247	254247	type	True	77.1245	92	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:45,454] [INFO] DFAST Taxonomy check result was written to GCF_003350455.1_ASM335045v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:45,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:45,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:45,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/checkm_data
[2024-01-24 11:05:45,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:45,490] [INFO] Task started: CheckM
[2024-01-24 11:05:45,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350455.1_ASM335045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350455.1_ASM335045v1_genomic.fna/checkm_input GCF_003350455.1_ASM335045v1_genomic.fna/checkm_result
[2024-01-24 11:06:10,290] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:10,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:10,311] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:10,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:10,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350455.1_ASM335045v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:10,313] [INFO] Task started: Blastn
[2024-01-24 11:06:10,313] [INFO] Running command: blastn -query GCF_003350455.1_ASM335045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4133cb55-d9b5-43b3-95ce-9320017b328a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350455.1_ASM335045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:11,455] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:11,458] [INFO] Selected 24 target genomes.
[2024-01-24 11:06:11,459] [INFO] Target genome list was writen to GCF_003350455.1_ASM335045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:11,476] [INFO] Task started: fastANI
[2024-01-24 11:06:11,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1eb605-550b-466b-9f1f-96031e9e6f60/GCF_003350455.1_ASM335045v1_genomic.fna.gz --refList GCF_003350455.1_ASM335045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350455.1_ASM335045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:22,245] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:22,251] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:22,251] [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_902459475.1	s__Aquicella lusitana	99.9902	805	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-16500;f__DSM-16500;g__Aquicella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_902459485.1	s__Aquicella_A siphonis	77.1245	92	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-16500;f__DSM-16500;g__Aquicella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:22,253] [INFO] GTDB search result was written to GCF_003350455.1_ASM335045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:22,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:22,255] [INFO] DFAST_QC result json was written to GCF_003350455.1_ASM335045v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:22,256] [INFO] DFAST_QC completed!
[2024-01-24 11:06:22,256] [INFO] Total running time: 0h0m57s