[2024-01-24 15:18:27,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference
[2024-01-24 15:18:28,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,913] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bc23483-4935-4236-9745-3808cf9d1d56/GCF_005222525.1_ASM522252v1_genomic.fna.gz | prodigal -d GCF_005222525.1_ASM522252v1_genomic.fna/cds.fna -a GCF_005222525.1_ASM522252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:38,802] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:38,803] [INFO] Task started: HMMsearch
[2024-01-24 15:18:38,803] [INFO] Running command: hmmsearch --tblout GCF_005222525.1_ASM522252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/reference_markers.hmm GCF_005222525.1_ASM522252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:39,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:39,059] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg4bc23483-4935-4236-9745-3808cf9d1d56/GCF_005222525.1_ASM522252v1_genomic.fna.gz]
[2024-01-24 15:18:39,101] [INFO] Query marker FASTA was written to GCF_005222525.1_ASM522252v1_genomic.fna/markers.fasta
[2024-01-24 15:18:39,101] [INFO] Task started: Blastn
[2024-01-24 15:18:39,101] [INFO] Running command: blastn -query GCF_005222525.1_ASM522252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/reference_markers.fasta -out GCF_005222525.1_ASM522252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:39,680] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:39,683] [INFO] Selected 2 target genomes.
[2024-01-24 15:18:39,684] [INFO] Target genome list was writen to GCF_005222525.1_ASM522252v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:39,686] [INFO] Task started: fastANI
[2024-01-24 15:18:39,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc23483-4935-4236-9745-3808cf9d1d56/GCF_005222525.1_ASM522252v1_genomic.fna.gz --refList GCF_005222525.1_ASM522252v1_genomic.fna/target_genomes.txt --output GCF_005222525.1_ASM522252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:41,108] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:41,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:41,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:41,113] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:41,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:41,113] [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
Metallosphaera prunae	strain=Ron 12/II	GCA_005222525.1	47304	47304	type	True	100.0	734	734	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:18:41,114] [INFO] DFAST Taxonomy check result was written to GCF_005222525.1_ASM522252v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:41,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:41,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:41,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/checkm_data
[2024-01-24 15:18:41,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:41,144] [INFO] Task started: CheckM
[2024-01-24 15:18:41,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005222525.1_ASM522252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005222525.1_ASM522252v1_genomic.fna/checkm_input GCF_005222525.1_ASM522252v1_genomic.fna/checkm_result
[2024-01-24 15:19:13,650] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:13,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:13,686] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:13,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:13,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005222525.1_ASM522252v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:13,688] [INFO] Task started: Blastn
[2024-01-24 15:19:13,688] [INFO] Running command: blastn -query GCF_005222525.1_ASM522252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab1c299-079c-44ef-b64b-c19b599fa981/dqc_reference/reference_markers_gtdb.fasta -out GCF_005222525.1_ASM522252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:14,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:14,159] [INFO] Selected 2 target genomes.
[2024-01-24 15:19:14,159] [INFO] Target genome list was writen to GCF_005222525.1_ASM522252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:14,163] [INFO] Task started: fastANI
[2024-01-24 15:19:14,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc23483-4935-4236-9745-3808cf9d1d56/GCF_005222525.1_ASM522252v1_genomic.fna.gz --refList GCF_005222525.1_ASM522252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005222525.1_ASM522252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:15,638] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:15,640] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:15,641] [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_000016605.1	s__Metallosphaera sedula	99.8906	719	734	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Metallosphaera	95.0	99.63	97.19	0.99	0.95	9	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:19:15,841] [INFO] GTDB search result was written to GCF_005222525.1_ASM522252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:15,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:15,845] [INFO] DFAST_QC result json was written to GCF_005222525.1_ASM522252v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:15,845] [INFO] DFAST_QC completed!
[2024-01-24 15:19:15,845] [INFO] Total running time: 0h0m48s