[2023-06-29 13:54:02,578] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:54:02,588] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:54:02,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgd138f011-5608-4817-bf55-5a6b6716225c/dqc_reference
[2023-06-29 13:54:03,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:54:03,920] [INFO] Task started: Prodigal
[2023-06-29 13:54:03,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg9deac31f-2e36-49bb-adfe-898bf47b3e87/GCA_023488405.1_ASM2348840v1_genomic.fna.gz | prodigal -d GCA_023488405.1_ASM2348840v1_genomic.fna/cds.fna -a GCA_023488405.1_ASM2348840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:54:05,425] [INFO] Task succeeded: Prodigal
[2023-06-29 13:54:05,426] [INFO] Task started: HMMsearch
[2023-06-29 13:54:05,426] [INFO] Running command: hmmsearch --tblout GCA_023488405.1_ASM2348840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd138f011-5608-4817-bf55-5a6b6716225c/dqc_reference/reference_markers.hmm GCA_023488405.1_ASM2348840v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:54:05,627] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:54:05,628] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg9deac31f-2e36-49bb-adfe-898bf47b3e87/GCA_023488405.1_ASM2348840v1_genomic.fna.gz]
[2023-06-29 13:54:05,638] [INFO] Query marker FASTA was written to GCA_023488405.1_ASM2348840v1_genomic.fna/markers.fasta
[2023-06-29 13:54:05,639] [INFO] Task started: Blastn
[2023-06-29 13:54:05,639] [INFO] Running command: blastn -query GCA_023488405.1_ASM2348840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd138f011-5608-4817-bf55-5a6b6716225c/dqc_reference/reference_markers.fasta -out GCA_023488405.1_ASM2348840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:54:06,119] [INFO] Task succeeded: Blastn
[2023-06-29 13:54:06,123] [INFO] Selected 0 target genomes.
[2023-06-29 13:54:06,123] [INFO] Target genome list was writen to GCA_023488405.1_ASM2348840v1_genomic.fna/target_genomes.txt
[2023-06-29 13:54:06,123] [ERROR] File is empty. [GCA_023488405.1_ASM2348840v1_genomic.fna/target_genomes.txt]
[2023-06-29 13:54:06,123] [ERROR] Task failed. No target genome found.
[2023-06-29 13:54:06,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:54:06,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd138f011-5608-4817-bf55-5a6b6716225c/dqc_reference/checkm_data
[2023-06-29 13:54:06,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:54:06,148] [INFO] Task started: CheckM
[2023-06-29 13:54:06,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023488405.1_ASM2348840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023488405.1_ASM2348840v1_genomic.fna/checkm_input GCA_023488405.1_ASM2348840v1_genomic.fna/checkm_result
[2023-06-29 13:54:19,296] [INFO] Task succeeded: CheckM
[2023-06-29 13:54:19,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:54:19,315] [INFO] ===== Completeness check finished =====
[2023-06-29 13:54:19,315] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:54:19,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023488405.1_ASM2348840v1_genomic.fna/markers.fasta)
[2023-06-29 13:54:19,316] [INFO] Task started: Blastn
[2023-06-29 13:54:19,316] [INFO] Running command: blastn -query GCA_023488405.1_ASM2348840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd138f011-5608-4817-bf55-5a6b6716225c/dqc_reference/reference_markers_gtdb.fasta -out GCA_023488405.1_ASM2348840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:54:19,788] [INFO] Task succeeded: Blastn
[2023-06-29 13:54:19,797] [INFO] Selected 1 target genomes.
[2023-06-29 13:54:19,797] [INFO] Target genome list was writen to GCA_023488405.1_ASM2348840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:54:19,798] [INFO] Task started: fastANI
[2023-06-29 13:54:19,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg9deac31f-2e36-49bb-adfe-898bf47b3e87/GCA_023488405.1_ASM2348840v1_genomic.fna.gz --refList GCA_023488405.1_ASM2348840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023488405.1_ASM2348840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:54:19,980] [INFO] Task succeeded: fastANI
[2023-06-29 13:54:19,982] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:54:19,982] [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 13:54:19,985] [INFO] GTDB search result was written to GCA_023488405.1_ASM2348840v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:54:19,985] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:54:19,988] [INFO] DFAST_QC result json was written to GCA_023488405.1_ASM2348840v1_genomic.fna/dqc_result.json
[2023-06-29 13:54:19,988] [INFO] DFAST_QC completed!
[2023-06-29 13:54:19,988] [INFO] Total running time: 0h0m17s