[2023-06-17 16:42:54,968] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:42:54,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:42:54,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a68d886-cd1c-403e-8fa3-7464da2dd454/dqc_reference
[2023-06-17 16:42:56,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:42:56,365] [INFO] Task started: Prodigal
[2023-06-17 16:42:56,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg95f0b2bb-1788-499a-98ec-dc7845659e87/GCA_003661905.1_ASM366190v1_genomic.fna.gz | prodigal -d GCA_003661905.1_ASM366190v1_genomic.fna/cds.fna -a GCA_003661905.1_ASM366190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:42:58,383] [INFO] Task succeeded: Prodigal
[2023-06-17 16:42:58,384] [INFO] Task started: HMMsearch
[2023-06-17 16:42:58,384] [INFO] Running command: hmmsearch --tblout GCA_003661905.1_ASM366190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a68d886-cd1c-403e-8fa3-7464da2dd454/dqc_reference/reference_markers.hmm GCA_003661905.1_ASM366190v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:42:58,592] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:42:58,594] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg95f0b2bb-1788-499a-98ec-dc7845659e87/GCA_003661905.1_ASM366190v1_genomic.fna.gz]
[2023-06-17 16:42:58,619] [INFO] Query marker FASTA was written to GCA_003661905.1_ASM366190v1_genomic.fna/markers.fasta
[2023-06-17 16:42:58,619] [INFO] Task started: Blastn
[2023-06-17 16:42:58,619] [INFO] Running command: blastn -query GCA_003661905.1_ASM366190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a68d886-cd1c-403e-8fa3-7464da2dd454/dqc_reference/reference_markers.fasta -out GCA_003661905.1_ASM366190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:42:59,550] [INFO] Task succeeded: Blastn
[2023-06-17 16:42:59,557] [INFO] Selected 0 target genomes.
[2023-06-17 16:42:59,557] [INFO] Target genome list was writen to GCA_003661905.1_ASM366190v1_genomic.fna/target_genomes.txt
[2023-06-17 16:42:59,557] [ERROR] File is empty. [GCA_003661905.1_ASM366190v1_genomic.fna/target_genomes.txt]
[2023-06-17 16:42:59,557] [ERROR] Task failed. No target genome found.
[2023-06-17 16:42:59,558] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:42:59,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a68d886-cd1c-403e-8fa3-7464da2dd454/dqc_reference/checkm_data
[2023-06-17 16:42:59,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:42:59,580] [INFO] Task started: CheckM
[2023-06-17 16:42:59,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003661905.1_ASM366190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003661905.1_ASM366190v1_genomic.fna/checkm_input GCA_003661905.1_ASM366190v1_genomic.fna/checkm_result
[2023-06-17 16:43:16,432] [INFO] Task succeeded: CheckM
[2023-06-17 16:43:16,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:43:16,455] [INFO] ===== Completeness check finished =====
[2023-06-17 16:43:16,456] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:43:16,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003661905.1_ASM366190v1_genomic.fna/markers.fasta)
[2023-06-17 16:43:16,457] [INFO] Task started: Blastn
[2023-06-17 16:43:16,457] [INFO] Running command: blastn -query GCA_003661905.1_ASM366190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a68d886-cd1c-403e-8fa3-7464da2dd454/dqc_reference/reference_markers_gtdb.fasta -out GCA_003661905.1_ASM366190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:16,965] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:16,970] [INFO] Selected 2 target genomes.
[2023-06-17 16:43:16,970] [INFO] Target genome list was writen to GCA_003661905.1_ASM366190v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:43:16,974] [INFO] Task started: fastANI
[2023-06-17 16:43:16,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f0b2bb-1788-499a-98ec-dc7845659e87/GCA_003661905.1_ASM366190v1_genomic.fna.gz --refList GCA_003661905.1_ASM366190v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003661905.1_ASM366190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:43:17,566] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:17,569] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:43:17,570] [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_003661905.1	s__B12-G17 sp003661905	100.0	322	325	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Ignisphaeraceae;g__B12-G17	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-17 16:43:17,572] [INFO] GTDB search result was written to GCA_003661905.1_ASM366190v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:43:17,572] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:43:17,575] [INFO] DFAST_QC result json was written to GCA_003661905.1_ASM366190v1_genomic.fna/dqc_result.json
[2023-06-17 16:43:17,575] [INFO] DFAST_QC completed!
[2023-06-17 16:43:17,575] [INFO] Total running time: 0h0m23s