[2023-06-04 19:38:18,479] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:18,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:18,487] [INFO] DQC Reference Directory: /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference
[2023-06-04 19:38:20,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:20,081] [INFO] Task started: Prodigal
[2023-06-04 19:38:20,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b30971-0388-427d-81fd-8df4bd17bc88/GCA_004145015.1_ASM414501v1_genomic.fna.gz | prodigal -d GCA_004145015.1_ASM414501v1_genomic.fna/cds.fna -a GCA_004145015.1_ASM414501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:24,217] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:24,218] [INFO] Task started: HMMsearch
[2023-06-04 19:38:24,218] [INFO] Running command: hmmsearch --tblout GCA_004145015.1_ASM414501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/reference_markers.hmm GCA_004145015.1_ASM414501v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:24,429] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:24,430] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg53b30971-0388-427d-81fd-8df4bd17bc88/GCA_004145015.1_ASM414501v1_genomic.fna.gz]
[2023-06-04 19:38:24,453] [INFO] Query marker FASTA was written to GCA_004145015.1_ASM414501v1_genomic.fna/markers.fasta
[2023-06-04 19:38:24,453] [INFO] Task started: Blastn
[2023-06-04 19:38:24,453] [INFO] Running command: blastn -query GCA_004145015.1_ASM414501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/reference_markers.fasta -out GCA_004145015.1_ASM414501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:25,233] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:25,237] [INFO] Selected 10 target genomes.
[2023-06-04 19:38:25,237] [INFO] Target genome list was writen to GCA_004145015.1_ASM414501v1_genomic.fna/target_genomes.txt
[2023-06-04 19:38:25,266] [INFO] Task started: fastANI
[2023-06-04 19:38:25,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b30971-0388-427d-81fd-8df4bd17bc88/GCA_004145015.1_ASM414501v1_genomic.fna.gz --refList GCA_004145015.1_ASM414501v1_genomic.fna/target_genomes.txt --output GCA_004145015.1_ASM414501v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:32,657] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:32,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:32,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:32,662] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:32,662] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 19:38:32,662] [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
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	82.0634	60	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:38:32,665] [INFO] DFAST Taxonomy check result was written to GCA_004145015.1_ASM414501v1_genomic.fna/tc_result.tsv
[2023-06-04 19:38:32,666] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:32,667] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:32,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/checkm_data
[2023-06-04 19:38:32,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:32,692] [INFO] Task started: CheckM
[2023-06-04 19:38:32,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004145015.1_ASM414501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004145015.1_ASM414501v1_genomic.fna/checkm_input GCA_004145015.1_ASM414501v1_genomic.fna/checkm_result
[2023-06-04 19:38:54,234] [INFO] Task succeeded: CheckM
[2023-06-04 19:38:54,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.86%
Contamintation: 57.38%
Strain heterogeneity: 42.19%
--------------------------------------------------------------------------------
[2023-06-04 19:38:54,264] [INFO] ===== Completeness check finished =====
[2023-06-04 19:38:54,265] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:38:54,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004145015.1_ASM414501v1_genomic.fna/markers.fasta)
[2023-06-04 19:38:54,265] [INFO] Task started: Blastn
[2023-06-04 19:38:54,266] [INFO] Running command: blastn -query GCA_004145015.1_ASM414501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3af1129-f103-4926-af94-0fe6ce441de1/dqc_reference/reference_markers_gtdb.fasta -out GCA_004145015.1_ASM414501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:54,917] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:54,925] [INFO] Selected 10 target genomes.
[2023-06-04 19:38:54,925] [INFO] Target genome list was writen to GCA_004145015.1_ASM414501v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:38:55,030] [INFO] Task started: fastANI
[2023-06-04 19:38:55,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b30971-0388-427d-81fd-8df4bd17bc88/GCA_004145015.1_ASM414501v1_genomic.fna.gz --refList GCA_004145015.1_ASM414501v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004145015.1_ASM414501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:39:01,229] [INFO] Task succeeded: fastANI
[2023-06-04 19:39:01,232] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 19:39:01,232] [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
--------------------------------------------------------------------------------
[2023-06-04 19:39:01,235] [INFO] GTDB search result was written to GCA_004145015.1_ASM414501v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:39:01,235] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:39:01,238] [INFO] DFAST_QC result json was written to GCA_004145015.1_ASM414501v1_genomic.fna/dqc_result.json
[2023-06-04 19:39:01,239] [INFO] DFAST_QC completed!
[2023-06-04 19:39:01,239] [INFO] Total running time: 0h0m43s