[2023-06-27 01:24:10,088] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:24:10,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:24:10,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a48378-20cb-4c15-8557-0f9f2d9448ef/dqc_reference
[2023-06-27 01:24:11,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:24:11,302] [INFO] Task started: Prodigal
[2023-06-27 01:24:11,303] [INFO] Running command: gunzip -c /var/lib/cwl/stga4760d70-e016-47d4-a898-bf63f747efdf/GCA_027492095.1_ASM2749209v1_genomic.fna.gz | prodigal -d GCA_027492095.1_ASM2749209v1_genomic.fna/cds.fna -a GCA_027492095.1_ASM2749209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:24:14,441] [INFO] Task succeeded: Prodigal
[2023-06-27 01:24:14,441] [INFO] Task started: HMMsearch
[2023-06-27 01:24:14,441] [INFO] Running command: hmmsearch --tblout GCA_027492095.1_ASM2749209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a48378-20cb-4c15-8557-0f9f2d9448ef/dqc_reference/reference_markers.hmm GCA_027492095.1_ASM2749209v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:24:14,642] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:24:14,644] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga4760d70-e016-47d4-a898-bf63f747efdf/GCA_027492095.1_ASM2749209v1_genomic.fna.gz]
[2023-06-27 01:24:14,674] [INFO] Query marker FASTA was written to GCA_027492095.1_ASM2749209v1_genomic.fna/markers.fasta
[2023-06-27 01:24:14,675] [INFO] Task started: Blastn
[2023-06-27 01:24:14,675] [INFO] Running command: blastn -query GCA_027492095.1_ASM2749209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a48378-20cb-4c15-8557-0f9f2d9448ef/dqc_reference/reference_markers.fasta -out GCA_027492095.1_ASM2749209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:24:15,152] [INFO] Task succeeded: Blastn
[2023-06-27 01:24:15,157] [INFO] Selected 0 target genomes.
[2023-06-27 01:24:15,157] [INFO] Target genome list was writen to GCA_027492095.1_ASM2749209v1_genomic.fna/target_genomes.txt
[2023-06-27 01:24:15,157] [ERROR] File is empty. [GCA_027492095.1_ASM2749209v1_genomic.fna/target_genomes.txt]
[2023-06-27 01:24:15,157] [ERROR] Task failed. No target genome found.
[2023-06-27 01:24:15,158] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:24:15,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a48378-20cb-4c15-8557-0f9f2d9448ef/dqc_reference/checkm_data
[2023-06-27 01:24:15,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:24:15,183] [INFO] Task started: CheckM
[2023-06-27 01:24:15,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027492095.1_ASM2749209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027492095.1_ASM2749209v1_genomic.fna/checkm_input GCA_027492095.1_ASM2749209v1_genomic.fna/checkm_result
[2023-06-27 01:24:32,336] [INFO] Task succeeded: CheckM
[2023-06-27 01:24:32,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:24:32,359] [INFO] ===== Completeness check finished =====
[2023-06-27 01:24:32,359] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:24:32,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027492095.1_ASM2749209v1_genomic.fna/markers.fasta)
[2023-06-27 01:24:32,360] [INFO] Task started: Blastn
[2023-06-27 01:24:32,360] [INFO] Running command: blastn -query GCA_027492095.1_ASM2749209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a48378-20cb-4c15-8557-0f9f2d9448ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_027492095.1_ASM2749209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:24:32,830] [INFO] Task succeeded: Blastn
[2023-06-27 01:24:32,834] [INFO] Selected 1 target genomes.
[2023-06-27 01:24:32,835] [INFO] Target genome list was writen to GCA_027492095.1_ASM2749209v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:24:32,838] [INFO] Task started: fastANI
[2023-06-27 01:24:32,838] [INFO] Running command: fastANI --query /var/lib/cwl/stga4760d70-e016-47d4-a898-bf63f747efdf/GCA_027492095.1_ASM2749209v1_genomic.fna.gz --refList GCA_027492095.1_ASM2749209v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027492095.1_ASM2749209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:24:33,581] [INFO] Task succeeded: fastANI
[2023-06-27 01:24:33,583] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:24:33,583] [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 01:24:33,585] [INFO] GTDB search result was written to GCA_027492095.1_ASM2749209v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:24:33,586] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:24:33,589] [INFO] DFAST_QC result json was written to GCA_027492095.1_ASM2749209v1_genomic.fna/dqc_result.json
[2023-06-27 01:24:33,590] [INFO] DFAST_QC completed!
[2023-06-27 01:24:33,590] [INFO] Total running time: 0h0m24s