[2023-06-29 05:14:18,774] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:14:18,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:14:18,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference
[2023-06-29 05:14:21,651] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:14:21,653] [INFO] Task started: Prodigal
[2023-06-29 05:14:21,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgf77e9578-10ac-4111-9bac-530e7be3edb6/GCA_027073875.1_ASM2707387v1_genomic.fna.gz | prodigal -d GCA_027073875.1_ASM2707387v1_genomic.fna/cds.fna -a GCA_027073875.1_ASM2707387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:14:30,012] [INFO] Task succeeded: Prodigal
[2023-06-29 05:14:30,012] [INFO] Task started: HMMsearch
[2023-06-29 05:14:30,013] [INFO] Running command: hmmsearch --tblout GCA_027073875.1_ASM2707387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/reference_markers.hmm GCA_027073875.1_ASM2707387v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:14:30,252] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:14:30,254] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf77e9578-10ac-4111-9bac-530e7be3edb6/GCA_027073875.1_ASM2707387v1_genomic.fna.gz]
[2023-06-29 05:14:30,281] [INFO] Query marker FASTA was written to GCA_027073875.1_ASM2707387v1_genomic.fna/markers.fasta
[2023-06-29 05:14:30,281] [INFO] Task started: Blastn
[2023-06-29 05:14:30,281] [INFO] Running command: blastn -query GCA_027073875.1_ASM2707387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/reference_markers.fasta -out GCA_027073875.1_ASM2707387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:14:30,871] [INFO] Task succeeded: Blastn
[2023-06-29 05:14:30,875] [INFO] Selected 24 target genomes.
[2023-06-29 05:14:30,875] [INFO] Target genome list was writen to GCA_027073875.1_ASM2707387v1_genomic.fna/target_genomes.txt
[2023-06-29 05:14:30,904] [INFO] Task started: fastANI
[2023-06-29 05:14:30,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77e9578-10ac-4111-9bac-530e7be3edb6/GCA_027073875.1_ASM2707387v1_genomic.fna.gz --refList GCA_027073875.1_ASM2707387v1_genomic.fna/target_genomes.txt --output GCA_027073875.1_ASM2707387v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:14:44,459] [INFO] Task succeeded: fastANI
[2023-06-29 05:14:44,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:14:44,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:14:44,462] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:14:44,462] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 05:14:44,462] [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
--------------------------------------------------------------------------------
[2023-06-29 05:14:44,464] [INFO] DFAST Taxonomy check result was written to GCA_027073875.1_ASM2707387v1_genomic.fna/tc_result.tsv
[2023-06-29 05:14:44,464] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:14:44,464] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:14:44,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/checkm_data
[2023-06-29 05:14:44,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:14:44,494] [INFO] Task started: CheckM
[2023-06-29 05:14:44,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027073875.1_ASM2707387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027073875.1_ASM2707387v1_genomic.fna/checkm_input GCA_027073875.1_ASM2707387v1_genomic.fna/checkm_result
[2023-06-29 05:15:14,893] [INFO] Task succeeded: CheckM
[2023-06-29 05:15:14,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.59%
Contamintation: 9.38%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 05:15:14,926] [INFO] ===== Completeness check finished =====
[2023-06-29 05:15:14,926] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:15:14,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027073875.1_ASM2707387v1_genomic.fna/markers.fasta)
[2023-06-29 05:15:14,927] [INFO] Task started: Blastn
[2023-06-29 05:15:14,927] [INFO] Running command: blastn -query GCA_027073875.1_ASM2707387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3ab5f1-bb70-4364-9b3f-5d137801507f/dqc_reference/reference_markers_gtdb.fasta -out GCA_027073875.1_ASM2707387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:15:15,685] [INFO] Task succeeded: Blastn
[2023-06-29 05:15:15,692] [INFO] Selected 31 target genomes.
[2023-06-29 05:15:15,692] [INFO] Target genome list was writen to GCA_027073875.1_ASM2707387v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:15:15,747] [INFO] Task started: fastANI
[2023-06-29 05:15:15,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77e9578-10ac-4111-9bac-530e7be3edb6/GCA_027073875.1_ASM2707387v1_genomic.fna.gz --refList GCA_027073875.1_ASM2707387v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027073875.1_ASM2707387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:15:31,070] [INFO] Task succeeded: fastANI
[2023-06-29 05:15:31,073] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 05:15:31,073] [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
--------------------------------------------------------------------------------
[2023-06-29 05:15:31,075] [INFO] GTDB search result was written to GCA_027073875.1_ASM2707387v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:15:31,076] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:15:31,079] [INFO] DFAST_QC result json was written to GCA_027073875.1_ASM2707387v1_genomic.fna/dqc_result.json
[2023-06-29 05:15:31,079] [INFO] DFAST_QC completed!
[2023-06-29 05:15:31,079] [INFO] Total running time: 0h1m12s