[2023-06-19 15:07:27,021] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:07:27,025] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:07:27,026] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa391985-1ab4-4a78-9387-d784664b726e/dqc_reference
[2023-06-19 15:07:28,292] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:07:28,296] [INFO] Task started: Prodigal
[2023-06-19 15:07:28,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dbe0a3e-cc18-4432-a50c-b3332ac59942/GCA_018692655.1_ASM1869265v1_genomic.fna.gz | prodigal -d GCA_018692655.1_ASM1869265v1_genomic.fna/cds.fna -a GCA_018692655.1_ASM1869265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:07:42,567] [INFO] Task succeeded: Prodigal
[2023-06-19 15:07:42,568] [INFO] Task started: HMMsearch
[2023-06-19 15:07:42,568] [INFO] Running command: hmmsearch --tblout GCA_018692655.1_ASM1869265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa391985-1ab4-4a78-9387-d784664b726e/dqc_reference/reference_markers.hmm GCA_018692655.1_ASM1869265v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:07:42,810] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:07:42,812] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5dbe0a3e-cc18-4432-a50c-b3332ac59942/GCA_018692655.1_ASM1869265v1_genomic.fna.gz]
[2023-06-19 15:07:42,847] [INFO] Query marker FASTA was written to GCA_018692655.1_ASM1869265v1_genomic.fna/markers.fasta
[2023-06-19 15:07:42,848] [INFO] Task started: Blastn
[2023-06-19 15:07:42,848] [INFO] Running command: blastn -query GCA_018692655.1_ASM1869265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa391985-1ab4-4a78-9387-d784664b726e/dqc_reference/reference_markers.fasta -out GCA_018692655.1_ASM1869265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:07:43,366] [INFO] Task succeeded: Blastn
[2023-06-19 15:07:43,380] [INFO] Selected 0 target genomes.
[2023-06-19 15:07:43,381] [INFO] Target genome list was writen to GCA_018692655.1_ASM1869265v1_genomic.fna/target_genomes.txt
[2023-06-19 15:07:43,381] [ERROR] File is empty. [GCA_018692655.1_ASM1869265v1_genomic.fna/target_genomes.txt]
[2023-06-19 15:07:43,381] [ERROR] Task failed. No target genome found.
[2023-06-19 15:07:43,381] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:07:43,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa391985-1ab4-4a78-9387-d784664b726e/dqc_reference/checkm_data
[2023-06-19 15:07:43,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:07:43,427] [INFO] Task started: CheckM
[2023-06-19 15:07:43,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018692655.1_ASM1869265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018692655.1_ASM1869265v1_genomic.fna/checkm_input GCA_018692655.1_ASM1869265v1_genomic.fna/checkm_result
[2023-06-19 15:08:27,737] [INFO] Task succeeded: CheckM
[2023-06-19 15:08:27,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:08:27,766] [INFO] ===== Completeness check finished =====
[2023-06-19 15:08:27,766] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:08:27,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018692655.1_ASM1869265v1_genomic.fna/markers.fasta)
[2023-06-19 15:08:27,767] [INFO] Task started: Blastn
[2023-06-19 15:08:27,767] [INFO] Running command: blastn -query GCA_018692655.1_ASM1869265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa391985-1ab4-4a78-9387-d784664b726e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018692655.1_ASM1869265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:08:28,220] [INFO] Task succeeded: Blastn
[2023-06-19 15:08:28,225] [INFO] Selected 3 target genomes.
[2023-06-19 15:08:28,225] [INFO] Target genome list was writen to GCA_018692655.1_ASM1869265v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:08:28,229] [INFO] Task started: fastANI
[2023-06-19 15:08:28,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dbe0a3e-cc18-4432-a50c-b3332ac59942/GCA_018692655.1_ASM1869265v1_genomic.fna.gz --refList GCA_018692655.1_ASM1869265v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018692655.1_ASM1869265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:08:29,581] [INFO] Task succeeded: fastANI
[2023-06-19 15:08:29,588] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:08:29,588] [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_018652685.1	s__RBG-16-57-9 sp018652685	99.7472	695	800	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__RBG-16-57-9	95.0	99.72	99.64	0.95	0.93	7	conclusive
GCA_013619005.1	s__RBG-16-57-9 sp013619005	81.9339	285	800	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__RBG-16-57-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:08:29,590] [INFO] GTDB search result was written to GCA_018692655.1_ASM1869265v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:08:29,591] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:08:29,594] [INFO] DFAST_QC result json was written to GCA_018692655.1_ASM1869265v1_genomic.fna/dqc_result.json
[2023-06-19 15:08:29,594] [INFO] DFAST_QC completed!
[2023-06-19 15:08:29,594] [INFO] Total running time: 0h1m3s