[2024-01-25 18:40:05,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference
[2024-01-25 18:40:06,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,611] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg95dcbff4-43df-48b4-bfc3-864342a549f7/GCF_001693775.2_ASM169377v2_genomic.fna.gz | prodigal -d GCF_001693775.2_ASM169377v2_genomic.fna/cds.fna -a GCF_001693775.2_ASM169377v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:10,177] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:10,178] [INFO] Task started: HMMsearch
[2024-01-25 18:40:10,178] [INFO] Running command: hmmsearch --tblout GCF_001693775.2_ASM169377v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/reference_markers.hmm GCF_001693775.2_ASM169377v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:10,355] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:10,356] [INFO] Found 6/6 markers.
[2024-01-25 18:40:10,378] [INFO] Query marker FASTA was written to GCF_001693775.2_ASM169377v2_genomic.fna/markers.fasta
[2024-01-25 18:40:10,378] [INFO] Task started: Blastn
[2024-01-25 18:40:10,378] [INFO] Running command: blastn -query GCF_001693775.2_ASM169377v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/reference_markers.fasta -out GCF_001693775.2_ASM169377v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:10,896] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:10,899] [INFO] Selected 15 target genomes.
[2024-01-25 18:40:10,899] [INFO] Target genome list was writen to GCF_001693775.2_ASM169377v2_genomic.fna/target_genomes.txt
[2024-01-25 18:40:10,905] [INFO] Task started: fastANI
[2024-01-25 18:40:10,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg95dcbff4-43df-48b4-bfc3-864342a549f7/GCF_001693775.2_ASM169377v2_genomic.fna.gz --refList GCF_001693775.2_ASM169377v2_genomic.fna/target_genomes.txt --output GCF_001693775.2_ASM169377v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:17,713] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:17,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:17,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:17,717] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:17,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:17,717] [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
Criibacterium bergeronii	strain=CCRI-22567	GCA_001693775.2	1871336	1871336	type	True	100.0	689	691	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:40:17,719] [INFO] DFAST Taxonomy check result was written to GCF_001693775.2_ASM169377v2_genomic.fna/tc_result.tsv
[2024-01-25 18:40:17,719] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:17,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:17,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/checkm_data
[2024-01-25 18:40:17,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:17,744] [INFO] Task started: CheckM
[2024-01-25 18:40:17,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001693775.2_ASM169377v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001693775.2_ASM169377v2_genomic.fna/checkm_input GCF_001693775.2_ASM169377v2_genomic.fna/checkm_result
[2024-01-25 18:40:34,471] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:34,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:34,491] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:34,492] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:34,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001693775.2_ASM169377v2_genomic.fna/markers.fasta)
[2024-01-25 18:40:34,492] [INFO] Task started: Blastn
[2024-01-25 18:40:34,492] [INFO] Running command: blastn -query GCF_001693775.2_ASM169377v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c7cc8d-d894-4b12-be2c-122624a7c263/dqc_reference/reference_markers_gtdb.fasta -out GCF_001693775.2_ASM169377v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:35,249] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:35,254] [INFO] Selected 17 target genomes.
[2024-01-25 18:40:35,254] [INFO] Target genome list was writen to GCF_001693775.2_ASM169377v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:35,275] [INFO] Task started: fastANI
[2024-01-25 18:40:35,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg95dcbff4-43df-48b4-bfc3-864342a549f7/GCF_001693775.2_ASM169377v2_genomic.fna.gz --refList GCF_001693775.2_ASM169377v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001693775.2_ASM169377v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:42,942] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:42,944] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:42,944] [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_001693775.2	s__Criibacterium bergeronii	100.0	689	691	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Criibacterium	95.0	98.89	98.57	0.88	0.88	3	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:40:42,948] [INFO] GTDB search result was written to GCF_001693775.2_ASM169377v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:42,948] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:42,950] [INFO] DFAST_QC result json was written to GCF_001693775.2_ASM169377v2_genomic.fna/dqc_result.json
[2024-01-25 18:40:42,950] [INFO] DFAST_QC completed!
[2024-01-25 18:40:42,950] [INFO] Total running time: 0h0m38s