[2023-06-28 15:42:22,456] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:42:22,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:42:22,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgf986db07-10f4-4538-892e-d9dcf16309fa/dqc_reference
[2023-06-28 15:42:23,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:42:23,685] [INFO] Task started: Prodigal
[2023-06-28 15:42:23,685] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc664fa2-77be-4b52-95b6-e473431f5851/GCA_020833565.1_ASM2083356v1_genomic.fna.gz | prodigal -d GCA_020833565.1_ASM2083356v1_genomic.fna/cds.fna -a GCA_020833565.1_ASM2083356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:42:25,158] [INFO] Task succeeded: Prodigal
[2023-06-28 15:42:25,159] [INFO] Task started: HMMsearch
[2023-06-28 15:42:25,159] [INFO] Running command: hmmsearch --tblout GCA_020833565.1_ASM2083356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf986db07-10f4-4538-892e-d9dcf16309fa/dqc_reference/reference_markers.hmm GCA_020833565.1_ASM2083356v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:42:25,340] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:42:25,342] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgcc664fa2-77be-4b52-95b6-e473431f5851/GCA_020833565.1_ASM2083356v1_genomic.fna.gz]
[2023-06-28 15:42:25,361] [INFO] Query marker FASTA was written to GCA_020833565.1_ASM2083356v1_genomic.fna/markers.fasta
[2023-06-28 15:42:25,361] [INFO] Task started: Blastn
[2023-06-28 15:42:25,361] [INFO] Running command: blastn -query GCA_020833565.1_ASM2083356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf986db07-10f4-4538-892e-d9dcf16309fa/dqc_reference/reference_markers.fasta -out GCA_020833565.1_ASM2083356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:42:25,841] [INFO] Task succeeded: Blastn
[2023-06-28 15:42:25,844] [INFO] Selected 0 target genomes.
[2023-06-28 15:42:25,844] [INFO] Target genome list was writen to GCA_020833565.1_ASM2083356v1_genomic.fna/target_genomes.txt
[2023-06-28 15:42:25,845] [ERROR] File is empty. [GCA_020833565.1_ASM2083356v1_genomic.fna/target_genomes.txt]
[2023-06-28 15:42:25,845] [ERROR] Task failed. No target genome found.
[2023-06-28 15:42:25,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:42:25,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf986db07-10f4-4538-892e-d9dcf16309fa/dqc_reference/checkm_data
[2023-06-28 15:42:25,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:42:25,863] [INFO] Task started: CheckM
[2023-06-28 15:42:25,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020833565.1_ASM2083356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020833565.1_ASM2083356v1_genomic.fna/checkm_input GCA_020833565.1_ASM2083356v1_genomic.fna/checkm_result
[2023-06-28 15:42:39,041] [INFO] Task succeeded: CheckM
[2023-06-28 15:42:39,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:42:39,066] [INFO] ===== Completeness check finished =====
[2023-06-28 15:42:39,066] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:42:39,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020833565.1_ASM2083356v1_genomic.fna/markers.fasta)
[2023-06-28 15:42:39,067] [INFO] Task started: Blastn
[2023-06-28 15:42:39,067] [INFO] Running command: blastn -query GCA_020833565.1_ASM2083356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf986db07-10f4-4538-892e-d9dcf16309fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_020833565.1_ASM2083356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:42:39,505] [INFO] Task succeeded: Blastn
[2023-06-28 15:42:39,509] [INFO] Selected 1 target genomes.
[2023-06-28 15:42:39,509] [INFO] Target genome list was writen to GCA_020833565.1_ASM2083356v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:42:39,512] [INFO] Task started: fastANI
[2023-06-28 15:42:39,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc664fa2-77be-4b52-95b6-e473431f5851/GCA_020833565.1_ASM2083356v1_genomic.fna.gz --refList GCA_020833565.1_ASM2083356v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020833565.1_ASM2083356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:42:39,871] [INFO] Task succeeded: fastANI
[2023-06-28 15:42:39,876] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:42:39,876] [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_009904015.1	s__WYEQ01 sp009904015	97.497	187	199	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Fervidicoccaceae;g__WYEQ01	95.0	96.59	96.59	0.95	0.95	2	conclusive
--------------------------------------------------------------------------------
[2023-06-28 15:42:39,878] [INFO] GTDB search result was written to GCA_020833565.1_ASM2083356v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:42:39,879] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:42:39,881] [INFO] DFAST_QC result json was written to GCA_020833565.1_ASM2083356v1_genomic.fna/dqc_result.json
[2023-06-28 15:42:39,881] [INFO] DFAST_QC completed!
[2023-06-28 15:42:39,881] [INFO] Total running time: 0h0m17s