[2023-06-27 03:10:16,275] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:10:16,279] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:10:16,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d134707-5667-4312-9d9d-c58867870b06/dqc_reference
[2023-06-27 03:10:17,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:10:17,865] [INFO] Task started: Prodigal
[2023-06-27 03:10:17,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg414b091c-cde4-4963-844d-28227a5f2b2e/GCA_002715545.1_ASM271554v1_genomic.fna.gz | prodigal -d GCA_002715545.1_ASM271554v1_genomic.fna/cds.fna -a GCA_002715545.1_ASM271554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:10:23,452] [INFO] Task succeeded: Prodigal
[2023-06-27 03:10:23,453] [INFO] Task started: HMMsearch
[2023-06-27 03:10:23,453] [INFO] Running command: hmmsearch --tblout GCA_002715545.1_ASM271554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d134707-5667-4312-9d9d-c58867870b06/dqc_reference/reference_markers.hmm GCA_002715545.1_ASM271554v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:10:23,698] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:10:23,699] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg414b091c-cde4-4963-844d-28227a5f2b2e/GCA_002715545.1_ASM271554v1_genomic.fna.gz]
[2023-06-27 03:10:23,733] [INFO] Query marker FASTA was written to GCA_002715545.1_ASM271554v1_genomic.fna/markers.fasta
[2023-06-27 03:10:23,733] [INFO] Task started: Blastn
[2023-06-27 03:10:23,734] [INFO] Running command: blastn -query GCA_002715545.1_ASM271554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d134707-5667-4312-9d9d-c58867870b06/dqc_reference/reference_markers.fasta -out GCA_002715545.1_ASM271554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:10:24,248] [INFO] Task succeeded: Blastn
[2023-06-27 03:10:24,255] [INFO] Selected 0 target genomes.
[2023-06-27 03:10:24,255] [INFO] Target genome list was writen to GCA_002715545.1_ASM271554v1_genomic.fna/target_genomes.txt
[2023-06-27 03:10:24,255] [ERROR] File is empty. [GCA_002715545.1_ASM271554v1_genomic.fna/target_genomes.txt]
[2023-06-27 03:10:24,255] [ERROR] Task failed. No target genome found.
[2023-06-27 03:10:24,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:10:24,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d134707-5667-4312-9d9d-c58867870b06/dqc_reference/checkm_data
[2023-06-27 03:10:24,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:10:24,294] [INFO] Task started: CheckM
[2023-06-27 03:10:24,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002715545.1_ASM271554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002715545.1_ASM271554v1_genomic.fna/checkm_input GCA_002715545.1_ASM271554v1_genomic.fna/checkm_result
[2023-06-27 03:10:49,494] [INFO] Task succeeded: CheckM
[2023-06-27 03:10:49,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:10:49,516] [INFO] ===== Completeness check finished =====
[2023-06-27 03:10:49,516] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:10:49,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002715545.1_ASM271554v1_genomic.fna/markers.fasta)
[2023-06-27 03:10:49,517] [INFO] Task started: Blastn
[2023-06-27 03:10:49,517] [INFO] Running command: blastn -query GCA_002715545.1_ASM271554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d134707-5667-4312-9d9d-c58867870b06/dqc_reference/reference_markers_gtdb.fasta -out GCA_002715545.1_ASM271554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:10:49,994] [INFO] Task succeeded: Blastn
[2023-06-27 03:10:50,009] [INFO] Selected 1 target genomes.
[2023-06-27 03:10:50,009] [INFO] Target genome list was writen to GCA_002715545.1_ASM271554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:10:50,035] [INFO] Task started: fastANI
[2023-06-27 03:10:50,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg414b091c-cde4-4963-844d-28227a5f2b2e/GCA_002715545.1_ASM271554v1_genomic.fna.gz --refList GCA_002715545.1_ASM271554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002715545.1_ASM271554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:10:50,694] [INFO] Task succeeded: fastANI
[2023-06-27 03:10:50,697] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 03:10:50,697] [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_002715545.1	s__SP79 sp002715545	100.0	610	614	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__SP79;g__SP79	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 03:10:50,699] [INFO] GTDB search result was written to GCA_002715545.1_ASM271554v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:10:50,699] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:10:50,702] [INFO] DFAST_QC result json was written to GCA_002715545.1_ASM271554v1_genomic.fna/dqc_result.json
[2023-06-27 03:10:50,702] [INFO] DFAST_QC completed!
[2023-06-27 03:10:50,702] [INFO] Total running time: 0h0m34s