[2023-06-29 13:22:09,879] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:22:09,881] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:22:09,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg04e60d3c-c49d-40e9-a092-15c98bf92e4e/dqc_reference
[2023-06-29 13:22:11,148] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:22:11,149] [INFO] Task started: Prodigal
[2023-06-29 13:22:11,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg431a090c-23ac-47f2-b506-a8bab4739398/GCA_023267785.1_ASM2326778v1_genomic.fna.gz | prodigal -d GCA_023267785.1_ASM2326778v1_genomic.fna/cds.fna -a GCA_023267785.1_ASM2326778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:22:13,798] [INFO] Task succeeded: Prodigal
[2023-06-29 13:22:13,798] [INFO] Task started: HMMsearch
[2023-06-29 13:22:13,799] [INFO] Running command: hmmsearch --tblout GCA_023267785.1_ASM2326778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04e60d3c-c49d-40e9-a092-15c98bf92e4e/dqc_reference/reference_markers.hmm GCA_023267785.1_ASM2326778v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:22:13,970] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:22:13,971] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg431a090c-23ac-47f2-b506-a8bab4739398/GCA_023267785.1_ASM2326778v1_genomic.fna.gz]
[2023-06-29 13:22:13,985] [INFO] Query marker FASTA was written to GCA_023267785.1_ASM2326778v1_genomic.fna/markers.fasta
[2023-06-29 13:22:13,985] [INFO] Task started: Blastn
[2023-06-29 13:22:13,985] [INFO] Running command: blastn -query GCA_023267785.1_ASM2326778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04e60d3c-c49d-40e9-a092-15c98bf92e4e/dqc_reference/reference_markers.fasta -out GCA_023267785.1_ASM2326778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:22:14,482] [INFO] Task succeeded: Blastn
[2023-06-29 13:22:14,486] [INFO] Selected 0 target genomes.
[2023-06-29 13:22:14,487] [INFO] Target genome list was writen to GCA_023267785.1_ASM2326778v1_genomic.fna/target_genomes.txt
[2023-06-29 13:22:14,487] [ERROR] File is empty. [GCA_023267785.1_ASM2326778v1_genomic.fna/target_genomes.txt]
[2023-06-29 13:22:14,487] [ERROR] Task failed. No target genome found.
[2023-06-29 13:22:14,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:22:14,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04e60d3c-c49d-40e9-a092-15c98bf92e4e/dqc_reference/checkm_data
[2023-06-29 13:22:14,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:22:14,504] [INFO] Task started: CheckM
[2023-06-29 13:22:14,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023267785.1_ASM2326778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023267785.1_ASM2326778v1_genomic.fna/checkm_input GCA_023267785.1_ASM2326778v1_genomic.fna/checkm_result
[2023-06-29 13:22:29,642] [INFO] Task succeeded: CheckM
[2023-06-29 13:22:29,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:22:29,662] [INFO] ===== Completeness check finished =====
[2023-06-29 13:22:29,663] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:22:29,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023267785.1_ASM2326778v1_genomic.fna/markers.fasta)
[2023-06-29 13:22:29,664] [INFO] Task started: Blastn
[2023-06-29 13:22:29,664] [INFO] Running command: blastn -query GCA_023267785.1_ASM2326778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04e60d3c-c49d-40e9-a092-15c98bf92e4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_023267785.1_ASM2326778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:22:30,231] [INFO] Task succeeded: Blastn
[2023-06-29 13:22:30,236] [INFO] Selected 4 target genomes.
[2023-06-29 13:22:30,236] [INFO] Target genome list was writen to GCA_023267785.1_ASM2326778v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:22:30,240] [INFO] Task started: fastANI
[2023-06-29 13:22:30,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg431a090c-23ac-47f2-b506-a8bab4739398/GCA_023267785.1_ASM2326778v1_genomic.fna.gz --refList GCA_023267785.1_ASM2326778v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023267785.1_ASM2326778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:22:31,743] [INFO] Task succeeded: fastANI
[2023-06-29 13:22:31,750] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:22:31,750] [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
--------------------------------------------------------------------------------
[2023-06-29 13:22:31,752] [INFO] GTDB search result was written to GCA_023267785.1_ASM2326778v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:22:31,753] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:22:31,755] [INFO] DFAST_QC result json was written to GCA_023267785.1_ASM2326778v1_genomic.fna/dqc_result.json
[2023-06-29 13:22:31,755] [INFO] DFAST_QC completed!
[2023-06-29 13:22:31,755] [INFO] Total running time: 0h0m22s