[2023-06-29 20:14:09,124] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:14:09,129] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:14:09,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference
[2023-06-29 20:14:10,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:14:10,458] [INFO] Task started: Prodigal
[2023-06-29 20:14:10,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a78ec96-caa5-4fa8-bb98-9f4072f710b7/GCA_023252995.1_ASM2325299v1_genomic.fna.gz | prodigal -d GCA_023252995.1_ASM2325299v1_genomic.fna/cds.fna -a GCA_023252995.1_ASM2325299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:20,729] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:20,729] [INFO] Task started: HMMsearch
[2023-06-29 20:14:20,730] [INFO] Running command: hmmsearch --tblout GCA_023252995.1_ASM2325299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/reference_markers.hmm GCA_023252995.1_ASM2325299v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:20,997] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:20,998] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9a78ec96-caa5-4fa8-bb98-9f4072f710b7/GCA_023252995.1_ASM2325299v1_genomic.fna.gz]
[2023-06-29 20:14:21,040] [INFO] Query marker FASTA was written to GCA_023252995.1_ASM2325299v1_genomic.fna/markers.fasta
[2023-06-29 20:14:21,040] [INFO] Task started: Blastn
[2023-06-29 20:14:21,040] [INFO] Running command: blastn -query GCA_023252995.1_ASM2325299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/reference_markers.fasta -out GCA_023252995.1_ASM2325299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:21,819] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:21,823] [INFO] Selected 22 target genomes.
[2023-06-29 20:14:21,824] [INFO] Target genome list was writen to GCA_023252995.1_ASM2325299v1_genomic.fna/target_genomes.txt
[2023-06-29 20:14:21,825] [INFO] Task started: fastANI
[2023-06-29 20:14:21,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a78ec96-caa5-4fa8-bb98-9f4072f710b7/GCA_023252995.1_ASM2325299v1_genomic.fna.gz --refList GCA_023252995.1_ASM2325299v1_genomic.fna/target_genomes.txt --output GCA_023252995.1_ASM2325299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:40,361] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:40,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:40,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:40,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:40,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:14:40,364] [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
--------------------------------------------------------------------------------
[2023-06-29 20:14:40,366] [INFO] DFAST Taxonomy check result was written to GCA_023252995.1_ASM2325299v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:40,367] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:40,367] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:40,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/checkm_data
[2023-06-29 20:14:40,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:40,402] [INFO] Task started: CheckM
[2023-06-29 20:14:40,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023252995.1_ASM2325299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023252995.1_ASM2325299v1_genomic.fna/checkm_input GCA_023252995.1_ASM2325299v1_genomic.fna/checkm_result
[2023-06-29 20:15:14,874] [INFO] Task succeeded: CheckM
[2023-06-29 20:15:14,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:15:14,897] [INFO] ===== Completeness check finished =====
[2023-06-29 20:15:14,897] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:15:14,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023252995.1_ASM2325299v1_genomic.fna/markers.fasta)
[2023-06-29 20:15:14,898] [INFO] Task started: Blastn
[2023-06-29 20:15:14,898] [INFO] Running command: blastn -query GCA_023252995.1_ASM2325299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d4fced0-56bb-44de-b45d-5dc8e9ddb191/dqc_reference/reference_markers_gtdb.fasta -out GCA_023252995.1_ASM2325299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:15,645] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:15,651] [INFO] Selected 25 target genomes.
[2023-06-29 20:15:15,651] [INFO] Target genome list was writen to GCA_023252995.1_ASM2325299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:15,660] [INFO] Task started: fastANI
[2023-06-29 20:15:15,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a78ec96-caa5-4fa8-bb98-9f4072f710b7/GCA_023252995.1_ASM2325299v1_genomic.fna.gz --refList GCA_023252995.1_ASM2325299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023252995.1_ASM2325299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:15:30,426] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:30,428] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:15:30,428] [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 20:15:30,431] [INFO] GTDB search result was written to GCA_023252995.1_ASM2325299v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:15:30,431] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:15:30,434] [INFO] DFAST_QC result json was written to GCA_023252995.1_ASM2325299v1_genomic.fna/dqc_result.json
[2023-06-29 20:15:30,434] [INFO] DFAST_QC completed!
[2023-06-29 20:15:30,435] [INFO] Total running time: 0h1m21s