[2023-06-29 12:58:11,983] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:58:11,986] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:58:11,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c304c9c-3e80-4eaf-be44-57730103dde9/dqc_reference
[2023-06-29 12:58:13,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:58:13,229] [INFO] Task started: Prodigal
[2023-06-29 12:58:13,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e2e627f-261d-44c9-b2bd-7a6678680c01/GCA_011043415.1_ASM1104341v1_genomic.fna.gz | prodigal -d GCA_011043415.1_ASM1104341v1_genomic.fna/cds.fna -a GCA_011043415.1_ASM1104341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:58:16,642] [INFO] Task succeeded: Prodigal
[2023-06-29 12:58:16,642] [INFO] Task started: HMMsearch
[2023-06-29 12:58:16,642] [INFO] Running command: hmmsearch --tblout GCA_011043415.1_ASM1104341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c304c9c-3e80-4eaf-be44-57730103dde9/dqc_reference/reference_markers.hmm GCA_011043415.1_ASM1104341v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:58:16,857] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:58:16,858] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg1e2e627f-261d-44c9-b2bd-7a6678680c01/GCA_011043415.1_ASM1104341v1_genomic.fna.gz]
[2023-06-29 12:58:16,875] [INFO] Query marker FASTA was written to GCA_011043415.1_ASM1104341v1_genomic.fna/markers.fasta
[2023-06-29 12:58:16,875] [INFO] Task started: Blastn
[2023-06-29 12:58:16,875] [INFO] Running command: blastn -query GCA_011043415.1_ASM1104341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c304c9c-3e80-4eaf-be44-57730103dde9/dqc_reference/reference_markers.fasta -out GCA_011043415.1_ASM1104341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:17,368] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:17,372] [INFO] Selected 0 target genomes.
[2023-06-29 12:58:17,372] [INFO] Target genome list was writen to GCA_011043415.1_ASM1104341v1_genomic.fna/target_genomes.txt
[2023-06-29 12:58:17,373] [ERROR] File is empty. [GCA_011043415.1_ASM1104341v1_genomic.fna/target_genomes.txt]
[2023-06-29 12:58:17,373] [ERROR] Task failed. No target genome found.
[2023-06-29 12:58:17,373] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:58:17,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c304c9c-3e80-4eaf-be44-57730103dde9/dqc_reference/checkm_data
[2023-06-29 12:58:17,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:58:17,395] [INFO] Task started: CheckM
[2023-06-29 12:58:17,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011043415.1_ASM1104341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011043415.1_ASM1104341v1_genomic.fna/checkm_input GCA_011043415.1_ASM1104341v1_genomic.fna/checkm_result
[2023-06-29 12:58:34,849] [INFO] Task succeeded: CheckM
[2023-06-29 12:58:34,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:58:34,871] [INFO] ===== Completeness check finished =====
[2023-06-29 12:58:34,871] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:58:34,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011043415.1_ASM1104341v1_genomic.fna/markers.fasta)
[2023-06-29 12:58:34,872] [INFO] Task started: Blastn
[2023-06-29 12:58:34,872] [INFO] Running command: blastn -query GCA_011043415.1_ASM1104341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c304c9c-3e80-4eaf-be44-57730103dde9/dqc_reference/reference_markers_gtdb.fasta -out GCA_011043415.1_ASM1104341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:35,361] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:35,365] [INFO] Selected 5 target genomes.
[2023-06-29 12:58:35,365] [INFO] Target genome list was writen to GCA_011043415.1_ASM1104341v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:58:35,369] [INFO] Task started: fastANI
[2023-06-29 12:58:35,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e2e627f-261d-44c9-b2bd-7a6678680c01/GCA_011043415.1_ASM1104341v1_genomic.fna.gz --refList GCA_011043415.1_ASM1104341v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011043415.1_ASM1104341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:58:36,815] [INFO] Task succeeded: fastANI
[2023-06-29 12:58:36,819] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:58:36,819] [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_011043415.1	s__B109-G9 sp003661505	100.0	339	346	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Geothermarchaeales;f__JDFR-13;g__B109-G9	95.0	99.16	99.04	0.83	0.82	3	conclusive
--------------------------------------------------------------------------------
[2023-06-29 12:58:36,821] [INFO] GTDB search result was written to GCA_011043415.1_ASM1104341v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:58:36,822] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:58:36,824] [INFO] DFAST_QC result json was written to GCA_011043415.1_ASM1104341v1_genomic.fna/dqc_result.json
[2023-06-29 12:58:36,824] [INFO] DFAST_QC completed!
[2023-06-29 12:58:36,824] [INFO] Total running time: 0h0m25s