[2024-01-24 14:31:00,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference
[2024-01-24 14:31:01,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,494] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,495] [INFO] Running command: gunzip -c /var/lib/cwl/stgf52c9112-795a-4b03-b36e-044517213d71/GCF_027921445.1_ASM2792144v1_genomic.fna.gz | prodigal -d GCF_027921445.1_ASM2792144v1_genomic.fna/cds.fna -a GCF_027921445.1_ASM2792144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:06,330] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:06,331] [INFO] Task started: HMMsearch
[2024-01-24 14:31:06,331] [INFO] Running command: hmmsearch --tblout GCF_027921445.1_ASM2792144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/reference_markers.hmm GCF_027921445.1_ASM2792144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:06,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:06,560] [INFO] Found 6/6 markers.
[2024-01-24 14:31:06,586] [INFO] Query marker FASTA was written to GCF_027921445.1_ASM2792144v1_genomic.fna/markers.fasta
[2024-01-24 14:31:06,587] [INFO] Task started: Blastn
[2024-01-24 14:31:06,587] [INFO] Running command: blastn -query GCF_027921445.1_ASM2792144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/reference_markers.fasta -out GCF_027921445.1_ASM2792144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:07,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:07,222] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:07,222] [INFO] Target genome list was writen to GCF_027921445.1_ASM2792144v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:07,233] [INFO] Task started: fastANI
[2024-01-24 14:31:07,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgf52c9112-795a-4b03-b36e-044517213d71/GCF_027921445.1_ASM2792144v1_genomic.fna.gz --refList GCF_027921445.1_ASM2792144v1_genomic.fna/target_genomes.txt --output GCF_027921445.1_ASM2792144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:19,733] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:19,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:19,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:19,738] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:19,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:19,738] [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
Peptoniphilus asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	79.4369	54	569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:19,740] [INFO] DFAST Taxonomy check result was written to GCF_027921445.1_ASM2792144v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:19,741] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:19,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:19,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/checkm_data
[2024-01-24 14:31:19,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:19,767] [INFO] Task started: CheckM
[2024-01-24 14:31:19,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921445.1_ASM2792144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921445.1_ASM2792144v1_genomic.fna/checkm_input GCF_027921445.1_ASM2792144v1_genomic.fna/checkm_result
[2024-01-24 14:31:42,418] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:42,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,436] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:42,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:42,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921445.1_ASM2792144v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:42,437] [INFO] Task started: Blastn
[2024-01-24 14:31:42,437] [INFO] Running command: blastn -query GCF_027921445.1_ASM2792144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95a4abe5-29e7-4780-b4b7-5d99564605c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921445.1_ASM2792144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,312] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,315] [INFO] Selected 26 target genomes.
[2024-01-24 14:31:43,315] [INFO] Target genome list was writen to GCF_027921445.1_ASM2792144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,339] [INFO] Task started: fastANI
[2024-01-24 14:31:43,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgf52c9112-795a-4b03-b36e-044517213d71/GCF_027921445.1_ASM2792144v1_genomic.fna.gz --refList GCF_027921445.1_ASM2792144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921445.1_ASM2792144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:55,116] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:55,119] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:31:55,119] [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
--------------------------------------------------------------------------------
[2024-01-24 14:31:55,121] [INFO] GTDB search result was written to GCF_027921445.1_ASM2792144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:55,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:55,124] [INFO] DFAST_QC result json was written to GCF_027921445.1_ASM2792144v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:55,124] [INFO] DFAST_QC completed!
[2024-01-24 14:31:55,124] [INFO] Total running time: 0h0m55s