[2023-06-29 14:28:32,959] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:28:32,961] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:28:32,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg35570b86-adc9-4db8-82e7-0321486829a6/dqc_reference
[2023-06-29 14:28:34,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:28:34,350] [INFO] Task started: Prodigal
[2023-06-29 14:28:34,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fb5ca21-2bf2-4f10-ad6f-14bfcf044403/GCA_011039455.1_ASM1103945v1_genomic.fna.gz | prodigal -d GCA_011039455.1_ASM1103945v1_genomic.fna/cds.fna -a GCA_011039455.1_ASM1103945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:28:37,656] [INFO] Task succeeded: Prodigal
[2023-06-29 14:28:37,657] [INFO] Task started: HMMsearch
[2023-06-29 14:28:37,657] [INFO] Running command: hmmsearch --tblout GCA_011039455.1_ASM1103945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35570b86-adc9-4db8-82e7-0321486829a6/dqc_reference/reference_markers.hmm GCA_011039455.1_ASM1103945v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:28:37,867] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:28:37,868] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8fb5ca21-2bf2-4f10-ad6f-14bfcf044403/GCA_011039455.1_ASM1103945v1_genomic.fna.gz]
[2023-06-29 14:28:37,891] [INFO] Query marker FASTA was written to GCA_011039455.1_ASM1103945v1_genomic.fna/markers.fasta
[2023-06-29 14:28:37,892] [INFO] Task started: Blastn
[2023-06-29 14:28:37,892] [INFO] Running command: blastn -query GCA_011039455.1_ASM1103945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35570b86-adc9-4db8-82e7-0321486829a6/dqc_reference/reference_markers.fasta -out GCA_011039455.1_ASM1103945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:28:38,395] [INFO] Task succeeded: Blastn
[2023-06-29 14:28:38,405] [INFO] Selected 0 target genomes.
[2023-06-29 14:28:38,405] [INFO] Target genome list was writen to GCA_011039455.1_ASM1103945v1_genomic.fna/target_genomes.txt
[2023-06-29 14:28:38,406] [ERROR] File is empty. [GCA_011039455.1_ASM1103945v1_genomic.fna/target_genomes.txt]
[2023-06-29 14:28:38,406] [ERROR] Task failed. No target genome found.
[2023-06-29 14:28:38,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:28:38,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35570b86-adc9-4db8-82e7-0321486829a6/dqc_reference/checkm_data
[2023-06-29 14:28:38,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:28:38,427] [INFO] Task started: CheckM
[2023-06-29 14:28:38,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011039455.1_ASM1103945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011039455.1_ASM1103945v1_genomic.fna/checkm_input GCA_011039455.1_ASM1103945v1_genomic.fna/checkm_result
[2023-06-29 14:28:56,900] [INFO] Task succeeded: CheckM
[2023-06-29 14:28:56,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.37%
Contamintation: 3.07%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 14:28:56,920] [INFO] ===== Completeness check finished =====
[2023-06-29 14:28:56,920] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:28:56,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011039455.1_ASM1103945v1_genomic.fna/markers.fasta)
[2023-06-29 14:28:56,921] [INFO] Task started: Blastn
[2023-06-29 14:28:56,921] [INFO] Running command: blastn -query GCA_011039455.1_ASM1103945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35570b86-adc9-4db8-82e7-0321486829a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_011039455.1_ASM1103945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:28:57,404] [INFO] Task succeeded: Blastn
[2023-06-29 14:28:57,408] [INFO] Selected 1 target genomes.
[2023-06-29 14:28:57,409] [INFO] Target genome list was writen to GCA_011039455.1_ASM1103945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:28:57,411] [INFO] Task started: fastANI
[2023-06-29 14:28:57,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb5ca21-2bf2-4f10-ad6f-14bfcf044403/GCA_011039455.1_ASM1103945v1_genomic.fna.gz --refList GCA_011039455.1_ASM1103945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011039455.1_ASM1103945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:28:57,648] [INFO] Task succeeded: fastANI
[2023-06-29 14:28:57,652] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:28:57,652] [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_003660635.1	s__EX4484-121 sp003660635	97.3081	96	138	d__Archaea;p__Thermoproteota;c__Nitrososphaeria_A;o__Caldarchaeales;f__NZ13-MGT;g__EX4484-121	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-29 14:28:57,654] [INFO] GTDB search result was written to GCA_011039455.1_ASM1103945v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:28:57,655] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:28:57,658] [INFO] DFAST_QC result json was written to GCA_011039455.1_ASM1103945v1_genomic.fna/dqc_result.json
[2023-06-29 14:28:57,658] [INFO] DFAST_QC completed!
[2023-06-29 14:28:57,658] [INFO] Total running time: 0h0m25s