[2023-06-27 17:41:05,492] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:05,498] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:05,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg26c0ccb4-b210-4bdd-abbd-2c506fb54c90/dqc_reference
[2023-06-27 17:41:08,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:08,729] [INFO] Task started: Prodigal
[2023-06-27 17:41:08,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ab3ca73-b16f-497b-9344-f173ba148967/GCA_027006115.1_ASM2700611v1_genomic.fna.gz | prodigal -d GCA_027006115.1_ASM2700611v1_genomic.fna/cds.fna -a GCA_027006115.1_ASM2700611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:10,949] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:10,950] [INFO] Task started: HMMsearch
[2023-06-27 17:41:10,950] [INFO] Running command: hmmsearch --tblout GCA_027006115.1_ASM2700611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26c0ccb4-b210-4bdd-abbd-2c506fb54c90/dqc_reference/reference_markers.hmm GCA_027006115.1_ASM2700611v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:11,252] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:11,253] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0ab3ca73-b16f-497b-9344-f173ba148967/GCA_027006115.1_ASM2700611v1_genomic.fna.gz]
[2023-06-27 17:41:11,273] [INFO] Query marker FASTA was written to GCA_027006115.1_ASM2700611v1_genomic.fna/markers.fasta
[2023-06-27 17:41:11,273] [INFO] Task started: Blastn
[2023-06-27 17:41:11,273] [INFO] Running command: blastn -query GCA_027006115.1_ASM2700611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26c0ccb4-b210-4bdd-abbd-2c506fb54c90/dqc_reference/reference_markers.fasta -out GCA_027006115.1_ASM2700611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:13,059] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:13,064] [INFO] Selected 0 target genomes.
[2023-06-27 17:41:13,064] [INFO] Target genome list was writen to GCA_027006115.1_ASM2700611v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:13,064] [ERROR] File is empty. [GCA_027006115.1_ASM2700611v1_genomic.fna/target_genomes.txt]
[2023-06-27 17:41:13,064] [ERROR] Task failed. No target genome found.
[2023-06-27 17:41:13,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:13,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26c0ccb4-b210-4bdd-abbd-2c506fb54c90/dqc_reference/checkm_data
[2023-06-27 17:41:13,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:13,084] [INFO] Task started: CheckM
[2023-06-27 17:41:13,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027006115.1_ASM2700611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027006115.1_ASM2700611v1_genomic.fna/checkm_input GCA_027006115.1_ASM2700611v1_genomic.fna/checkm_result
[2023-06-27 17:41:30,846] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:30,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.45%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:30,868] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:30,868] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:30,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027006115.1_ASM2700611v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:30,869] [INFO] Task started: Blastn
[2023-06-27 17:41:30,869] [INFO] Running command: blastn -query GCA_027006115.1_ASM2700611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26c0ccb4-b210-4bdd-abbd-2c506fb54c90/dqc_reference/reference_markers_gtdb.fasta -out GCA_027006115.1_ASM2700611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:31,384] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:31,405] [INFO] Selected 2 target genomes.
[2023-06-27 17:41:31,406] [INFO] Target genome list was writen to GCA_027006115.1_ASM2700611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:41:31,409] [INFO] Task started: fastANI
[2023-06-27 17:41:31,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab3ca73-b16f-497b-9344-f173ba148967/GCA_027006115.1_ASM2700611v1_genomic.fna.gz --refList GCA_027006115.1_ASM2700611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027006115.1_ASM2700611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:41:31,941] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:31,944] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:41:31,944] [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_015521095.1	s__S143-63 sp015521095	98.7006	126	142	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Acidilobaceae;g__S143-63	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 17:41:31,948] [INFO] GTDB search result was written to GCA_027006115.1_ASM2700611v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:41:31,948] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:41:31,951] [INFO] DFAST_QC result json was written to GCA_027006115.1_ASM2700611v1_genomic.fna/dqc_result.json
[2023-06-27 17:41:31,952] [INFO] DFAST_QC completed!
[2023-06-27 17:41:31,952] [INFO] Total running time: 0h0m26s