[2024-01-24 12:13:29,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:29,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:29,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference
[2024-01-24 12:13:30,471] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,472] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg77baa9ab-84e8-4f90-828f-416a61de91aa/GCF_008274215.1_ASM827421v1_genomic.fna.gz | prodigal -d GCF_008274215.1_ASM827421v1_genomic.fna/cds.fna -a GCF_008274215.1_ASM827421v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:36,355] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:36,356] [INFO] Task started: HMMsearch
[2024-01-24 12:13:36,356] [INFO] Running command: hmmsearch --tblout GCF_008274215.1_ASM827421v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/reference_markers.hmm GCF_008274215.1_ASM827421v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:36,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:36,622] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77baa9ab-84e8-4f90-828f-416a61de91aa/GCF_008274215.1_ASM827421v1_genomic.fna.gz]
[2024-01-24 12:13:36,644] [INFO] Query marker FASTA was written to GCF_008274215.1_ASM827421v1_genomic.fna/markers.fasta
[2024-01-24 12:13:36,645] [INFO] Task started: Blastn
[2024-01-24 12:13:36,645] [INFO] Running command: blastn -query GCF_008274215.1_ASM827421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/reference_markers.fasta -out GCF_008274215.1_ASM827421v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:37,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:37,288] [INFO] Selected 9 target genomes.
[2024-01-24 12:13:37,289] [INFO] Target genome list was writen to GCF_008274215.1_ASM827421v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:37,295] [INFO] Task started: fastANI
[2024-01-24 12:13:37,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg77baa9ab-84e8-4f90-828f-416a61de91aa/GCF_008274215.1_ASM827421v1_genomic.fna.gz --refList GCF_008274215.1_ASM827421v1_genomic.fna/target_genomes.txt --output GCF_008274215.1_ASM827421v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:40,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:40,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:40,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:40,967] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:40,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:40,968] [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
Calorimonas adulescens	strain=A05MB	GCA_008274215.1	2606906	2606906	type	True	100.0	834	837	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:13:40,969] [INFO] DFAST Taxonomy check result was written to GCF_008274215.1_ASM827421v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:40,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:40,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:40,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/checkm_data
[2024-01-24 12:13:40,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:40,999] [INFO] Task started: CheckM
[2024-01-24 12:13:40,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008274215.1_ASM827421v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008274215.1_ASM827421v1_genomic.fna/checkm_input GCF_008274215.1_ASM827421v1_genomic.fna/checkm_result
[2024-01-24 12:14:05,002] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:05,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:05,021] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:05,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:05,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008274215.1_ASM827421v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:05,023] [INFO] Task started: Blastn
[2024-01-24 12:14:05,023] [INFO] Running command: blastn -query GCF_008274215.1_ASM827421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c646da-bb70-4341-89f3-609c94eb1e84/dqc_reference/reference_markers_gtdb.fasta -out GCF_008274215.1_ASM827421v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:05,852] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:05,855] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:05,856] [INFO] Target genome list was writen to GCF_008274215.1_ASM827421v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:05,982] [INFO] Task started: fastANI
[2024-01-24 12:14:05,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg77baa9ab-84e8-4f90-828f-416a61de91aa/GCF_008274215.1_ASM827421v1_genomic.fna.gz --refList GCF_008274215.1_ASM827421v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008274215.1_ASM827421v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:14,158] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,163] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:14,163] [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_008274215.1	s__Calorimonas adulescens	100.0	834	837	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__UBA4877;g__Calorimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,165] [INFO] GTDB search result was written to GCF_008274215.1_ASM827421v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:14,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:14,167] [INFO] DFAST_QC result json was written to GCF_008274215.1_ASM827421v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:14,168] [INFO] DFAST_QC completed!
[2024-01-24 12:14:14,168] [INFO] Total running time: 0h0m45s