[2023-06-18 21:39:27,920] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:39:27,922] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:39:27,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference
[2023-06-18 21:39:29,196] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:39:29,197] [INFO] Task started: Prodigal
[2023-06-18 21:39:29,197] [INFO] Running command: gunzip -c /var/lib/cwl/stg77f35d1f-edeb-4ba1-8a9a-c908d0019fc3/GCA_018606745.1_ASM1860674v1_genomic.fna.gz | prodigal -d GCA_018606745.1_ASM1860674v1_genomic.fna/cds.fna -a GCA_018606745.1_ASM1860674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:39:29,909] [INFO] Task succeeded: Prodigal
[2023-06-18 21:39:29,909] [INFO] Task started: HMMsearch
[2023-06-18 21:39:29,910] [INFO] Running command: hmmsearch --tblout GCA_018606745.1_ASM1860674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/reference_markers.hmm GCA_018606745.1_ASM1860674v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:39:30,078] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:39:30,079] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg77f35d1f-edeb-4ba1-8a9a-c908d0019fc3/GCA_018606745.1_ASM1860674v1_genomic.fna.gz]
[2023-06-18 21:39:30,095] [INFO] Query marker FASTA was written to GCA_018606745.1_ASM1860674v1_genomic.fna/markers.fasta
[2023-06-18 21:39:30,095] [INFO] Task started: Blastn
[2023-06-18 21:39:30,095] [INFO] Running command: blastn -query GCA_018606745.1_ASM1860674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/reference_markers.fasta -out GCA_018606745.1_ASM1860674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:30,583] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:30,589] [INFO] Selected 13 target genomes.
[2023-06-18 21:39:30,589] [INFO] Target genome list was writen to GCA_018606745.1_ASM1860674v1_genomic.fna/target_genomes.txt
[2023-06-18 21:39:30,596] [INFO] Task started: fastANI
[2023-06-18 21:39:30,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f35d1f-edeb-4ba1-8a9a-c908d0019fc3/GCA_018606745.1_ASM1860674v1_genomic.fna.gz --refList GCA_018606745.1_ASM1860674v1_genomic.fna/target_genomes.txt --output GCA_018606745.1_ASM1860674v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:34,211] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:34,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:34,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:34,218] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 21:39:34,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 21:39:34,218] [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
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.9519	115	121	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.9244	116	121	95	conclusive
--------------------------------------------------------------------------------
[2023-06-18 21:39:34,223] [INFO] DFAST Taxonomy check result was written to GCA_018606745.1_ASM1860674v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:34,223] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:34,223] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:34,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/checkm_data
[2023-06-18 21:39:34,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:34,238] [INFO] Task started: CheckM
[2023-06-18 21:39:34,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018606745.1_ASM1860674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018606745.1_ASM1860674v1_genomic.fna/checkm_input GCA_018606745.1_ASM1860674v1_genomic.fna/checkm_result
[2023-06-18 21:39:44,601] [INFO] Task succeeded: CheckM
[2023-06-18 21:39:44,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:39:44,623] [INFO] ===== Completeness check finished =====
[2023-06-18 21:39:44,624] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:39:44,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018606745.1_ASM1860674v1_genomic.fna/markers.fasta)
[2023-06-18 21:39:44,624] [INFO] Task started: Blastn
[2023-06-18 21:39:44,625] [INFO] Running command: blastn -query GCA_018606745.1_ASM1860674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4868e4-1ddb-49fe-a999-f846887801bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018606745.1_ASM1860674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:45,033] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:45,037] [INFO] Selected 12 target genomes.
[2023-06-18 21:39:45,037] [INFO] Target genome list was writen to GCA_018606745.1_ASM1860674v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:39:45,043] [INFO] Task started: fastANI
[2023-06-18 21:39:45,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f35d1f-edeb-4ba1-8a9a-c908d0019fc3/GCA_018606745.1_ASM1860674v1_genomic.fna.gz --refList GCA_018606745.1_ASM1860674v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018606745.1_ASM1860674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:39:48,614] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:48,619] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:39:48,619] [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
GCF_000160875.1	s__Lactobacillus iners	98.9244	116	121	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
--------------------------------------------------------------------------------
[2023-06-18 21:39:48,621] [INFO] GTDB search result was written to GCA_018606745.1_ASM1860674v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:39:48,623] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:39:48,629] [INFO] DFAST_QC result json was written to GCA_018606745.1_ASM1860674v1_genomic.fna/dqc_result.json
[2023-06-18 21:39:48,630] [INFO] DFAST_QC completed!
[2023-06-18 21:39:48,630] [INFO] Total running time: 0h0m21s