[2023-06-17 01:33:18,416] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:33:18,429] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:33:18,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e35c9a-f0c3-4c5f-b94a-45d0313aaae6/dqc_reference
[2023-06-17 01:33:19,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:33:19,753] [INFO] Task started: Prodigal
[2023-06-17 01:33:19,753] [INFO] Running command: gunzip -c /var/lib/cwl/stgac5811de-38cd-4d94-88b1-c41e2fd3c669/GCA_003662685.1_ASM366268v1_genomic.fna.gz | prodigal -d GCA_003662685.1_ASM366268v1_genomic.fna/cds.fna -a GCA_003662685.1_ASM366268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:33:23,345] [INFO] Task succeeded: Prodigal
[2023-06-17 01:33:23,346] [INFO] Task started: HMMsearch
[2023-06-17 01:33:23,346] [INFO] Running command: hmmsearch --tblout GCA_003662685.1_ASM366268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e35c9a-f0c3-4c5f-b94a-45d0313aaae6/dqc_reference/reference_markers.hmm GCA_003662685.1_ASM366268v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:33:23,579] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:33:23,581] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgac5811de-38cd-4d94-88b1-c41e2fd3c669/GCA_003662685.1_ASM366268v1_genomic.fna.gz]
[2023-06-17 01:33:23,644] [INFO] Query marker FASTA was written to GCA_003662685.1_ASM366268v1_genomic.fna/markers.fasta
[2023-06-17 01:33:23,645] [INFO] Task started: Blastn
[2023-06-17 01:33:23,645] [INFO] Running command: blastn -query GCA_003662685.1_ASM366268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e35c9a-f0c3-4c5f-b94a-45d0313aaae6/dqc_reference/reference_markers.fasta -out GCA_003662685.1_ASM366268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:33:24,170] [INFO] Task succeeded: Blastn
[2023-06-17 01:33:24,174] [INFO] Selected 0 target genomes.
[2023-06-17 01:33:24,175] [INFO] Target genome list was writen to GCA_003662685.1_ASM366268v1_genomic.fna/target_genomes.txt
[2023-06-17 01:33:24,175] [ERROR] File is empty. [GCA_003662685.1_ASM366268v1_genomic.fna/target_genomes.txt]
[2023-06-17 01:33:24,175] [ERROR] Task failed. No target genome found.
[2023-06-17 01:33:24,176] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:33:24,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e35c9a-f0c3-4c5f-b94a-45d0313aaae6/dqc_reference/checkm_data
[2023-06-17 01:33:24,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:33:24,222] [INFO] Task started: CheckM
[2023-06-17 01:33:24,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003662685.1_ASM366268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003662685.1_ASM366268v1_genomic.fna/checkm_input GCA_003662685.1_ASM366268v1_genomic.fna/checkm_result
[2023-06-17 01:33:43,525] [INFO] Task succeeded: CheckM
[2023-06-17 01:33:43,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.92%
Contamintation: 10.19%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-17 01:33:43,572] [INFO] ===== Completeness check finished =====
[2023-06-17 01:33:43,573] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:33:43,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003662685.1_ASM366268v1_genomic.fna/markers.fasta)
[2023-06-17 01:33:43,574] [INFO] Task started: Blastn
[2023-06-17 01:33:43,574] [INFO] Running command: blastn -query GCA_003662685.1_ASM366268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e35c9a-f0c3-4c5f-b94a-45d0313aaae6/dqc_reference/reference_markers_gtdb.fasta -out GCA_003662685.1_ASM366268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:33:44,228] [INFO] Task succeeded: Blastn
[2023-06-17 01:33:44,232] [INFO] Selected 3 target genomes.
[2023-06-17 01:33:44,233] [INFO] Target genome list was writen to GCA_003662685.1_ASM366268v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:33:44,236] [INFO] Task started: fastANI
[2023-06-17 01:33:44,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgac5811de-38cd-4d94-88b1-c41e2fd3c669/GCA_003662685.1_ASM366268v1_genomic.fna.gz --refList GCA_003662685.1_ASM366268v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003662685.1_ASM366268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:33:45,271] [INFO] Task succeeded: fastANI
[2023-06-17 01:33:45,275] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:33:45,275] [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_003661975.1	s__B63 sp003661975	89.5443	160	388	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__B26-1;g__B63	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:33:45,283] [INFO] GTDB search result was written to GCA_003662685.1_ASM366268v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:33:45,284] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:33:45,287] [INFO] DFAST_QC result json was written to GCA_003662685.1_ASM366268v1_genomic.fna/dqc_result.json
[2023-06-17 01:33:45,287] [INFO] DFAST_QC completed!
[2023-06-17 01:33:45,287] [INFO] Total running time: 0h0m27s