[2023-06-27 11:41:29,636] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:41:29,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:41:29,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference
[2023-06-27 11:41:30,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:41:30,991] [INFO] Task started: Prodigal
[2023-06-27 11:41:30,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg511368f3-e801-4983-8e6d-d06ee4df6b40/GCA_026983085.1_ASM2698308v1_genomic.fna.gz | prodigal -d GCA_026983085.1_ASM2698308v1_genomic.fna/cds.fna -a GCA_026983085.1_ASM2698308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:41:32,985] [INFO] Task succeeded: Prodigal
[2023-06-27 11:41:32,986] [INFO] Task started: HMMsearch
[2023-06-27 11:41:32,986] [INFO] Running command: hmmsearch --tblout GCA_026983085.1_ASM2698308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/reference_markers.hmm GCA_026983085.1_ASM2698308v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:41:33,172] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:41:33,174] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg511368f3-e801-4983-8e6d-d06ee4df6b40/GCA_026983085.1_ASM2698308v1_genomic.fna.gz]
[2023-06-27 11:41:33,194] [INFO] Query marker FASTA was written to GCA_026983085.1_ASM2698308v1_genomic.fna/markers.fasta
[2023-06-27 11:41:33,195] [INFO] Task started: Blastn
[2023-06-27 11:41:33,195] [INFO] Running command: blastn -query GCA_026983085.1_ASM2698308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/reference_markers.fasta -out GCA_026983085.1_ASM2698308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:33,838] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:33,852] [INFO] Selected 12 target genomes.
[2023-06-27 11:41:33,853] [INFO] Target genome list was writen to GCA_026983085.1_ASM2698308v1_genomic.fna/target_genomes.txt
[2023-06-27 11:41:33,856] [INFO] Task started: fastANI
[2023-06-27 11:41:33,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg511368f3-e801-4983-8e6d-d06ee4df6b40/GCA_026983085.1_ASM2698308v1_genomic.fna.gz --refList GCA_026983085.1_ASM2698308v1_genomic.fna/target_genomes.txt --output GCA_026983085.1_ASM2698308v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:41:38,994] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:38,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:41:38,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:41:38,996] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:41:38,997] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:41:38,997] [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
--------------------------------------------------------------------------------
[2023-06-27 11:41:38,999] [INFO] DFAST Taxonomy check result was written to GCA_026983085.1_ASM2698308v1_genomic.fna/tc_result.tsv
[2023-06-27 11:41:38,999] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:41:39,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:41:39,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/checkm_data
[2023-06-27 11:41:39,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:41:39,021] [INFO] Task started: CheckM
[2023-06-27 11:41:39,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026983085.1_ASM2698308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026983085.1_ASM2698308v1_genomic.fna/checkm_input GCA_026983085.1_ASM2698308v1_genomic.fna/checkm_result
[2023-06-27 11:41:54,745] [INFO] Task succeeded: CheckM
[2023-06-27 11:41:54,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.60%
Contamintation: 5.06%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-27 11:41:54,777] [INFO] ===== Completeness check finished =====
[2023-06-27 11:41:54,778] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:41:54,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026983085.1_ASM2698308v1_genomic.fna/markers.fasta)
[2023-06-27 11:41:54,779] [INFO] Task started: Blastn
[2023-06-27 11:41:54,779] [INFO] Running command: blastn -query GCA_026983085.1_ASM2698308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49fcedb6-ed8a-47ab-aabd-1258b76a68db/dqc_reference/reference_markers_gtdb.fasta -out GCA_026983085.1_ASM2698308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:55,506] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:55,511] [INFO] Selected 19 target genomes.
[2023-06-27 11:41:55,512] [INFO] Target genome list was writen to GCA_026983085.1_ASM2698308v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:41:55,528] [INFO] Task started: fastANI
[2023-06-27 11:41:55,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg511368f3-e801-4983-8e6d-d06ee4df6b40/GCA_026983085.1_ASM2698308v1_genomic.fna.gz --refList GCA_026983085.1_ASM2698308v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026983085.1_ASM2698308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:42:03,102] [INFO] Task succeeded: fastANI
[2023-06-27 11:42:03,104] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:42:03,104] [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
--------------------------------------------------------------------------------
[2023-06-27 11:42:03,113] [INFO] GTDB search result was written to GCA_026983085.1_ASM2698308v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:42:03,114] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:42:03,117] [INFO] DFAST_QC result json was written to GCA_026983085.1_ASM2698308v1_genomic.fna/dqc_result.json
[2023-06-27 11:42:03,117] [INFO] DFAST_QC completed!
[2023-06-27 11:42:03,117] [INFO] Total running time: 0h0m33s