[2023-07-01 02:45:53,882] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:45:53,884] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:45:53,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference
[2023-07-01 02:45:55,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:45:55,184] [INFO] Task started: Prodigal
[2023-07-01 02:45:55,185] [INFO] Running command: gunzip -c /var/lib/cwl/stga853cb37-19fb-4f67-92b8-8618d059a33f/GCA_016208005.1_ASM1620800v1_genomic.fna.gz | prodigal -d GCA_016208005.1_ASM1620800v1_genomic.fna/cds.fna -a GCA_016208005.1_ASM1620800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:46:03,995] [INFO] Task succeeded: Prodigal
[2023-07-01 02:46:03,995] [INFO] Task started: HMMsearch
[2023-07-01 02:46:03,996] [INFO] Running command: hmmsearch --tblout GCA_016208005.1_ASM1620800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/reference_markers.hmm GCA_016208005.1_ASM1620800v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:46:04,232] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:46:04,234] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga853cb37-19fb-4f67-92b8-8618d059a33f/GCA_016208005.1_ASM1620800v1_genomic.fna.gz]
[2023-07-01 02:46:04,270] [INFO] Query marker FASTA was written to GCA_016208005.1_ASM1620800v1_genomic.fna/markers.fasta
[2023-07-01 02:46:04,270] [INFO] Task started: Blastn
[2023-07-01 02:46:04,270] [INFO] Running command: blastn -query GCA_016208005.1_ASM1620800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/reference_markers.fasta -out GCA_016208005.1_ASM1620800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:46:04,867] [INFO] Task succeeded: Blastn
[2023-07-01 02:46:04,872] [INFO] Selected 12 target genomes.
[2023-07-01 02:46:04,873] [INFO] Target genome list was writen to GCA_016208005.1_ASM1620800v1_genomic.fna/target_genomes.txt
[2023-07-01 02:46:04,877] [INFO] Task started: fastANI
[2023-07-01 02:46:04,878] [INFO] Running command: fastANI --query /var/lib/cwl/stga853cb37-19fb-4f67-92b8-8618d059a33f/GCA_016208005.1_ASM1620800v1_genomic.fna.gz --refList GCA_016208005.1_ASM1620800v1_genomic.fna/target_genomes.txt --output GCA_016208005.1_ASM1620800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:46:13,257] [INFO] Task succeeded: fastANI
[2023-07-01 02:46:13,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:46:13,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:46:13,259] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:46:13,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 02:46:13,259] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-07-01 02:46:13,261] [INFO] DFAST Taxonomy check result was written to GCA_016208005.1_ASM1620800v1_genomic.fna/tc_result.tsv
[2023-07-01 02:46:13,262] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:46:13,262] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:46:13,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/checkm_data
[2023-07-01 02:46:13,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:46:13,301] [INFO] Task started: CheckM
[2023-07-01 02:46:13,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016208005.1_ASM1620800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016208005.1_ASM1620800v1_genomic.fna/checkm_input GCA_016208005.1_ASM1620800v1_genomic.fna/checkm_result
[2023-07-01 02:46:42,557] [INFO] Task succeeded: CheckM
[2023-07-01 02:46:42,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:46:42,578] [INFO] ===== Completeness check finished =====
[2023-07-01 02:46:42,579] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:46:42,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016208005.1_ASM1620800v1_genomic.fna/markers.fasta)
[2023-07-01 02:46:42,579] [INFO] Task started: Blastn
[2023-07-01 02:46:42,579] [INFO] Running command: blastn -query GCA_016208005.1_ASM1620800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead85b6c-9611-49af-bc00-02083bbb07e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_016208005.1_ASM1620800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:46:43,033] [INFO] Task succeeded: Blastn
[2023-07-01 02:46:43,037] [INFO] Selected 14 target genomes.
[2023-07-01 02:46:43,037] [INFO] Target genome list was writen to GCA_016208005.1_ASM1620800v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:46:43,053] [INFO] Task started: fastANI
[2023-07-01 02:46:43,053] [INFO] Running command: fastANI --query /var/lib/cwl/stga853cb37-19fb-4f67-92b8-8618d059a33f/GCA_016208005.1_ASM1620800v1_genomic.fna.gz --refList GCA_016208005.1_ASM1620800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016208005.1_ASM1620800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:46:49,517] [INFO] Task succeeded: fastANI
[2023-07-01 02:46:49,522] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:46:49,523] [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_016215705.1	s__JACRIR01 sp016215705	78.6803	405	856	d__Bacteria;p__Abyssubacteria;c__SURF-5;o__SURF-5;f__SURF-5;g__JACRIR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:46:49,525] [INFO] GTDB search result was written to GCA_016208005.1_ASM1620800v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:46:49,526] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:46:49,529] [INFO] DFAST_QC result json was written to GCA_016208005.1_ASM1620800v1_genomic.fna/dqc_result.json
[2023-07-01 02:46:49,529] [INFO] DFAST_QC completed!
[2023-07-01 02:46:49,529] [INFO] Total running time: 0h0m56s