[2023-06-28 17:55:51,902] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:55:51,905] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:55:51,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg1736668a-abba-4700-9af6-c432e7a0a620/dqc_reference
[2023-06-28 17:55:53,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:55:53,349] [INFO] Task started: Prodigal
[2023-06-28 17:55:53,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg0925beb2-c9a0-4d8c-95fb-aecf2a15fc11/GCA_020833145.1_ASM2083314v1_genomic.fna.gz | prodigal -d GCA_020833145.1_ASM2083314v1_genomic.fna/cds.fna -a GCA_020833145.1_ASM2083314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:55:55,182] [INFO] Task succeeded: Prodigal
[2023-06-28 17:55:55,183] [INFO] Task started: HMMsearch
[2023-06-28 17:55:55,183] [INFO] Running command: hmmsearch --tblout GCA_020833145.1_ASM2083314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1736668a-abba-4700-9af6-c432e7a0a620/dqc_reference/reference_markers.hmm GCA_020833145.1_ASM2083314v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:55:55,321] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:55:55,322] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0925beb2-c9a0-4d8c-95fb-aecf2a15fc11/GCA_020833145.1_ASM2083314v1_genomic.fna.gz]
[2023-06-28 17:55:55,337] [INFO] Query marker FASTA was written to GCA_020833145.1_ASM2083314v1_genomic.fna/markers.fasta
[2023-06-28 17:55:55,337] [INFO] Task started: Blastn
[2023-06-28 17:55:55,337] [INFO] Running command: blastn -query GCA_020833145.1_ASM2083314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1736668a-abba-4700-9af6-c432e7a0a620/dqc_reference/reference_markers.fasta -out GCA_020833145.1_ASM2083314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:55:55,799] [INFO] Task succeeded: Blastn
[2023-06-28 17:55:55,803] [INFO] Selected 0 target genomes.
[2023-06-28 17:55:55,804] [INFO] Target genome list was writen to GCA_020833145.1_ASM2083314v1_genomic.fna/target_genomes.txt
[2023-06-28 17:55:55,804] [ERROR] File is empty. [GCA_020833145.1_ASM2083314v1_genomic.fna/target_genomes.txt]
[2023-06-28 17:55:55,804] [ERROR] Task failed. No target genome found.
[2023-06-28 17:55:55,804] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:55:55,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1736668a-abba-4700-9af6-c432e7a0a620/dqc_reference/checkm_data
[2023-06-28 17:55:55,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:55:55,822] [INFO] Task started: CheckM
[2023-06-28 17:55:55,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020833145.1_ASM2083314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020833145.1_ASM2083314v1_genomic.fna/checkm_input GCA_020833145.1_ASM2083314v1_genomic.fna/checkm_result
[2023-06-28 17:56:11,450] [INFO] Task succeeded: CheckM
[2023-06-28 17:56:11,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:56:11,472] [INFO] ===== Completeness check finished =====
[2023-06-28 17:56:11,473] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:56:11,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020833145.1_ASM2083314v1_genomic.fna/markers.fasta)
[2023-06-28 17:56:11,473] [INFO] Task started: Blastn
[2023-06-28 17:56:11,473] [INFO] Running command: blastn -query GCA_020833145.1_ASM2083314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1736668a-abba-4700-9af6-c432e7a0a620/dqc_reference/reference_markers_gtdb.fasta -out GCA_020833145.1_ASM2083314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:56:11,978] [INFO] Task succeeded: Blastn
[2023-06-28 17:56:11,982] [INFO] Selected 1 target genomes.
[2023-06-28 17:56:11,983] [INFO] Target genome list was writen to GCA_020833145.1_ASM2083314v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:56:11,985] [INFO] Task started: fastANI
[2023-06-28 17:56:11,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg0925beb2-c9a0-4d8c-95fb-aecf2a15fc11/GCA_020833145.1_ASM2083314v1_genomic.fna.gz --refList GCA_020833145.1_ASM2083314v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020833145.1_ASM2083314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:56:12,483] [INFO] Task succeeded: fastANI
[2023-06-28 17:56:12,486] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:56:12,486] [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
GCA_009903825.1	s__WYEN01 sp009903825	98.5352	299	328	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__AG1;g__WYEN01	95.0	97.03	97.03	0.77	0.77	2	conclusive
--------------------------------------------------------------------------------
[2023-06-28 17:56:12,489] [INFO] GTDB search result was written to GCA_020833145.1_ASM2083314v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:56:12,490] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:56:12,493] [INFO] DFAST_QC result json was written to GCA_020833145.1_ASM2083314v1_genomic.fna/dqc_result.json
[2023-06-28 17:56:12,494] [INFO] DFAST_QC completed!
[2023-06-28 17:56:12,494] [INFO] Total running time: 0h0m21s