[2023-06-26 23:34:34,654] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:34:34,656] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:34:34,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg7350279e-ecb1-4fa8-b338-c90358d6b189/dqc_reference
[2023-06-26 23:34:37,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:34:37,587] [INFO] Task started: Prodigal
[2023-06-26 23:34:37,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b286270-f807-44a4-a46f-6ff9474cedec/GCA_026397015.1_ASM2639701v1_genomic.fna.gz | prodigal -d GCA_026397015.1_ASM2639701v1_genomic.fna/cds.fna -a GCA_026397015.1_ASM2639701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:34:42,064] [INFO] Task succeeded: Prodigal
[2023-06-26 23:34:42,066] [INFO] Task started: HMMsearch
[2023-06-26 23:34:42,066] [INFO] Running command: hmmsearch --tblout GCA_026397015.1_ASM2639701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7350279e-ecb1-4fa8-b338-c90358d6b189/dqc_reference/reference_markers.hmm GCA_026397015.1_ASM2639701v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:34:42,266] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:34:42,268] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg9b286270-f807-44a4-a46f-6ff9474cedec/GCA_026397015.1_ASM2639701v1_genomic.fna.gz]
[2023-06-26 23:34:42,284] [INFO] Query marker FASTA was written to GCA_026397015.1_ASM2639701v1_genomic.fna/markers.fasta
[2023-06-26 23:34:42,284] [INFO] Task started: Blastn
[2023-06-26 23:34:42,284] [INFO] Running command: blastn -query GCA_026397015.1_ASM2639701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7350279e-ecb1-4fa8-b338-c90358d6b189/dqc_reference/reference_markers.fasta -out GCA_026397015.1_ASM2639701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:34:42,774] [INFO] Task succeeded: Blastn
[2023-06-26 23:34:42,779] [INFO] Selected 0 target genomes.
[2023-06-26 23:34:42,780] [INFO] Target genome list was writen to GCA_026397015.1_ASM2639701v1_genomic.fna/target_genomes.txt
[2023-06-26 23:34:42,781] [ERROR] File is empty. [GCA_026397015.1_ASM2639701v1_genomic.fna/target_genomes.txt]
[2023-06-26 23:34:42,781] [ERROR] Task failed. No target genome found.
[2023-06-26 23:34:42,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:34:42,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7350279e-ecb1-4fa8-b338-c90358d6b189/dqc_reference/checkm_data
[2023-06-26 23:34:42,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:34:42,808] [INFO] Task started: CheckM
[2023-06-26 23:34:42,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026397015.1_ASM2639701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026397015.1_ASM2639701v1_genomic.fna/checkm_input GCA_026397015.1_ASM2639701v1_genomic.fna/checkm_result
[2023-06-26 23:35:03,390] [INFO] Task succeeded: CheckM
[2023-06-26 23:35:03,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:35:03,415] [INFO] ===== Completeness check finished =====
[2023-06-26 23:35:03,416] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:35:03,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026397015.1_ASM2639701v1_genomic.fna/markers.fasta)
[2023-06-26 23:35:03,417] [INFO] Task started: Blastn
[2023-06-26 23:35:03,417] [INFO] Running command: blastn -query GCA_026397015.1_ASM2639701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7350279e-ecb1-4fa8-b338-c90358d6b189/dqc_reference/reference_markers_gtdb.fasta -out GCA_026397015.1_ASM2639701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:35:03,943] [INFO] Task succeeded: Blastn
[2023-06-26 23:35:03,947] [INFO] Selected 1 target genomes.
[2023-06-26 23:35:03,948] [INFO] Target genome list was writen to GCA_026397015.1_ASM2639701v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:35:03,951] [INFO] Task started: fastANI
[2023-06-26 23:35:03,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b286270-f807-44a4-a46f-6ff9474cedec/GCA_026397015.1_ASM2639701v1_genomic.fna.gz --refList GCA_026397015.1_ASM2639701v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026397015.1_ASM2639701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:35:04,190] [INFO] Task succeeded: fastANI
[2023-06-26 23:35:04,192] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:35:04,193] [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
--------------------------------------------------------------------------------
[2023-06-26 23:35:04,196] [INFO] GTDB search result was written to GCA_026397015.1_ASM2639701v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:35:04,197] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:35:04,201] [INFO] DFAST_QC result json was written to GCA_026397015.1_ASM2639701v1_genomic.fna/dqc_result.json
[2023-06-26 23:35:04,201] [INFO] DFAST_QC completed!
[2023-06-26 23:35:04,201] [INFO] Total running time: 0h0m30s