[2023-06-17 12:24:29,912] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:29,914] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:29,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg873fc7cb-4851-474c-b553-6244f5e45c27/dqc_reference
[2023-06-17 12:24:31,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:31,140] [INFO] Task started: Prodigal
[2023-06-17 12:24:31,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg560c00b8-5856-440f-9831-c365b80c496b/GCA_013154205.1_ASM1315420v1_genomic.fna.gz | prodigal -d GCA_013154205.1_ASM1315420v1_genomic.fna/cds.fna -a GCA_013154205.1_ASM1315420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:34,286] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:34,287] [INFO] Task started: HMMsearch
[2023-06-17 12:24:34,287] [INFO] Running command: hmmsearch --tblout GCA_013154205.1_ASM1315420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg873fc7cb-4851-474c-b553-6244f5e45c27/dqc_reference/reference_markers.hmm GCA_013154205.1_ASM1315420v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:34,432] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:34,433] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg560c00b8-5856-440f-9831-c365b80c496b/GCA_013154205.1_ASM1315420v1_genomic.fna.gz]
[2023-06-17 12:24:34,467] [INFO] Query marker FASTA was written to GCA_013154205.1_ASM1315420v1_genomic.fna/markers.fasta
[2023-06-17 12:24:34,467] [INFO] Task started: Blastn
[2023-06-17 12:24:34,467] [INFO] Running command: blastn -query GCA_013154205.1_ASM1315420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg873fc7cb-4851-474c-b553-6244f5e45c27/dqc_reference/reference_markers.fasta -out GCA_013154205.1_ASM1315420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:34,929] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:34,939] [INFO] Selected 0 target genomes.
[2023-06-17 12:24:34,939] [INFO] Target genome list was writen to GCA_013154205.1_ASM1315420v1_genomic.fna/target_genomes.txt
[2023-06-17 12:24:34,939] [ERROR] File is empty. [GCA_013154205.1_ASM1315420v1_genomic.fna/target_genomes.txt]
[2023-06-17 12:24:34,940] [ERROR] Task failed. No target genome found.
[2023-06-17 12:24:34,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:24:34,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg873fc7cb-4851-474c-b553-6244f5e45c27/dqc_reference/checkm_data
[2023-06-17 12:24:34,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:24:34,973] [INFO] Task started: CheckM
[2023-06-17 12:24:34,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013154205.1_ASM1315420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013154205.1_ASM1315420v1_genomic.fna/checkm_input GCA_013154205.1_ASM1315420v1_genomic.fna/checkm_result
[2023-06-17 12:24:52,814] [INFO] Task succeeded: CheckM
[2023-06-17 12:24:52,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:24:52,834] [INFO] ===== Completeness check finished =====
[2023-06-17 12:24:52,835] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:24:52,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013154205.1_ASM1315420v1_genomic.fna/markers.fasta)
[2023-06-17 12:24:52,835] [INFO] Task started: Blastn
[2023-06-17 12:24:52,835] [INFO] Running command: blastn -query GCA_013154205.1_ASM1315420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg873fc7cb-4851-474c-b553-6244f5e45c27/dqc_reference/reference_markers_gtdb.fasta -out GCA_013154205.1_ASM1315420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:53,259] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:53,263] [INFO] Selected 4 target genomes.
[2023-06-17 12:24:53,263] [INFO] Target genome list was writen to GCA_013154205.1_ASM1315420v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:24:53,268] [INFO] Task started: fastANI
[2023-06-17 12:24:53,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg560c00b8-5856-440f-9831-c365b80c496b/GCA_013154205.1_ASM1315420v1_genomic.fna.gz --refList GCA_013154205.1_ASM1315420v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013154205.1_ASM1315420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:24:54,470] [INFO] Task succeeded: fastANI
[2023-06-17 12:24:54,473] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:24:54,473] [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_013154205.1	s__JAADCY01 sp013154205	100.0	504	512	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Desulfurococcaceae;g__JAADCY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-17 12:24:54,476] [INFO] GTDB search result was written to GCA_013154205.1_ASM1315420v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:24:54,476] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:24:54,478] [INFO] DFAST_QC result json was written to GCA_013154205.1_ASM1315420v1_genomic.fna/dqc_result.json
[2023-06-17 12:24:54,479] [INFO] DFAST_QC completed!
[2023-06-17 12:24:54,479] [INFO] Total running time: 0h0m25s