[2023-06-17 13:27:53,005] [INFO] DFAST_QC pipeline started.
[2023-06-17 13:27:53,008] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 13:27:53,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference
[2023-06-17 13:27:54,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 13:27:54,837] [INFO] Task started: Prodigal
[2023-06-17 13:27:54,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg967496d8-0474-43b2-999f-383ceadfde40/GCA_009784425.1_ASM978442v1_genomic.fna.gz | prodigal -d GCA_009784425.1_ASM978442v1_genomic.fna/cds.fna -a GCA_009784425.1_ASM978442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 13:28:00,101] [INFO] Task succeeded: Prodigal
[2023-06-17 13:28:00,102] [INFO] Task started: HMMsearch
[2023-06-17 13:28:00,102] [INFO] Running command: hmmsearch --tblout GCA_009784425.1_ASM978442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/reference_markers.hmm GCA_009784425.1_ASM978442v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 13:28:00,324] [INFO] Task succeeded: HMMsearch
[2023-06-17 13:28:00,326] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg967496d8-0474-43b2-999f-383ceadfde40/GCA_009784425.1_ASM978442v1_genomic.fna.gz]
[2023-06-17 13:28:00,351] [INFO] Query marker FASTA was written to GCA_009784425.1_ASM978442v1_genomic.fna/markers.fasta
[2023-06-17 13:28:00,351] [INFO] Task started: Blastn
[2023-06-17 13:28:00,351] [INFO] Running command: blastn -query GCA_009784425.1_ASM978442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/reference_markers.fasta -out GCA_009784425.1_ASM978442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:28:00,987] [INFO] Task succeeded: Blastn
[2023-06-17 13:28:00,990] [INFO] Selected 15 target genomes.
[2023-06-17 13:28:00,991] [INFO] Target genome list was writen to GCA_009784425.1_ASM978442v1_genomic.fna/target_genomes.txt
[2023-06-17 13:28:00,994] [INFO] Task started: fastANI
[2023-06-17 13:28:00,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg967496d8-0474-43b2-999f-383ceadfde40/GCA_009784425.1_ASM978442v1_genomic.fna.gz --refList GCA_009784425.1_ASM978442v1_genomic.fna/target_genomes.txt --output GCA_009784425.1_ASM978442v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 13:28:08,304] [INFO] Task succeeded: fastANI
[2023-06-17 13:28:08,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 13:28:08,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 13:28:08,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 13:28:08,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 13:28:08,308] [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
--------------------------------------------------------------------------------
[2023-06-17 13:28:08,311] [INFO] DFAST Taxonomy check result was written to GCA_009784425.1_ASM978442v1_genomic.fna/tc_result.tsv
[2023-06-17 13:28:08,312] [INFO] ===== Taxonomy check completed =====
[2023-06-17 13:28:08,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 13:28:08,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/checkm_data
[2023-06-17 13:28:08,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 13:28:08,344] [INFO] Task started: CheckM
[2023-06-17 13:28:08,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009784425.1_ASM978442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009784425.1_ASM978442v1_genomic.fna/checkm_input GCA_009784425.1_ASM978442v1_genomic.fna/checkm_result
[2023-06-17 13:28:31,358] [INFO] Task succeeded: CheckM
[2023-06-17 13:28:31,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 13:28:31,390] [INFO] ===== Completeness check finished =====
[2023-06-17 13:28:31,390] [INFO] ===== Start GTDB Search =====
[2023-06-17 13:28:31,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009784425.1_ASM978442v1_genomic.fna/markers.fasta)
[2023-06-17 13:28:31,391] [INFO] Task started: Blastn
[2023-06-17 13:28:31,391] [INFO] Running command: blastn -query GCA_009784425.1_ASM978442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fcda6ee-a918-463e-ba88-8728033b9db2/dqc_reference/reference_markers_gtdb.fasta -out GCA_009784425.1_ASM978442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:28:32,179] [INFO] Task succeeded: Blastn
[2023-06-17 13:28:32,183] [INFO] Selected 16 target genomes.
[2023-06-17 13:28:32,184] [INFO] Target genome list was writen to GCA_009784425.1_ASM978442v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 13:28:32,195] [INFO] Task started: fastANI
[2023-06-17 13:28:32,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg967496d8-0474-43b2-999f-383ceadfde40/GCA_009784425.1_ASM978442v1_genomic.fna.gz --refList GCA_009784425.1_ASM978442v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009784425.1_ASM978442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 13:28:38,461] [INFO] Task succeeded: fastANI
[2023-06-17 13:28:38,468] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 13:28:38,468] [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_009784425.1	s__WQXH01 sp009784425	100.0	589	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UBA8131;g__WQXH01	95.0	99.67	99.67	0.86	0.86	2	conclusive
GCA_009784945.1	s__WQXH01 sp009784945	76.8745	107	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__UBA8131;g__WQXH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 13:28:38,470] [INFO] GTDB search result was written to GCA_009784425.1_ASM978442v1_genomic.fna/result_gtdb.tsv
[2023-06-17 13:28:38,471] [INFO] ===== GTDB Search completed =====
[2023-06-17 13:28:38,474] [INFO] DFAST_QC result json was written to GCA_009784425.1_ASM978442v1_genomic.fna/dqc_result.json
[2023-06-17 13:28:38,474] [INFO] DFAST_QC completed!
[2023-06-17 13:28:38,474] [INFO] Total running time: 0h0m45s