[2023-06-13 17:56:02,506] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:56:02,507] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:56:02,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference
[2023-06-13 17:56:03,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:56:03,655] [INFO] Task started: Prodigal
[2023-06-13 17:56:03,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg11d51a7d-49ed-48e0-8743-cabf4ac5bd6f/GCA_022754405.1_ASM2275440v1_genomic.fna.gz | prodigal -d GCA_022754405.1_ASM2275440v1_genomic.fna/cds.fna -a GCA_022754405.1_ASM2275440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:56:04,111] [INFO] Task succeeded: Prodigal
[2023-06-13 17:56:04,111] [INFO] Task started: HMMsearch
[2023-06-13 17:56:04,111] [INFO] Running command: hmmsearch --tblout GCA_022754405.1_ASM2275440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/reference_markers.hmm GCA_022754405.1_ASM2275440v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:56:04,280] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:56:04,281] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg11d51a7d-49ed-48e0-8743-cabf4ac5bd6f/GCA_022754405.1_ASM2275440v1_genomic.fna.gz]
[2023-06-13 17:56:04,296] [INFO] Query marker FASTA was written to GCA_022754405.1_ASM2275440v1_genomic.fna/markers.fasta
[2023-06-13 17:56:04,296] [INFO] Task started: Blastn
[2023-06-13 17:56:04,297] [INFO] Running command: blastn -query GCA_022754405.1_ASM2275440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/reference_markers.fasta -out GCA_022754405.1_ASM2275440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:04,795] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:04,801] [INFO] Selected 13 target genomes.
[2023-06-13 17:56:04,801] [INFO] Target genome list was writen to GCA_022754405.1_ASM2275440v1_genomic.fna/target_genomes.txt
[2023-06-13 17:56:04,802] [INFO] Task started: fastANI
[2023-06-13 17:56:04,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d51a7d-49ed-48e0-8743-cabf4ac5bd6f/GCA_022754405.1_ASM2275440v1_genomic.fna.gz --refList GCA_022754405.1_ASM2275440v1_genomic.fna/target_genomes.txt --output GCA_022754405.1_ASM2275440v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:08,513] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:08,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:08,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:08,519] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 17:56:08,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 17:56:08,519] [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
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	99.1461	86	90	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	99.1329	88	90	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 17:56:08,521] [INFO] DFAST Taxonomy check result was written to GCA_022754405.1_ASM2275440v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:08,521] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:08,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:08,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/checkm_data
[2023-06-13 17:56:08,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:08,529] [INFO] Task started: CheckM
[2023-06-13 17:56:08,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022754405.1_ASM2275440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022754405.1_ASM2275440v1_genomic.fna/checkm_input GCA_022754405.1_ASM2275440v1_genomic.fna/checkm_result
[2023-06-13 17:56:17,049] [INFO] Task succeeded: CheckM
[2023-06-13 17:56:17,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:56:17,119] [INFO] ===== Completeness check finished =====
[2023-06-13 17:56:17,120] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:56:17,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022754405.1_ASM2275440v1_genomic.fna/markers.fasta)
[2023-06-13 17:56:17,120] [INFO] Task started: Blastn
[2023-06-13 17:56:17,120] [INFO] Running command: blastn -query GCA_022754405.1_ASM2275440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb9dc50-0ba1-4470-b4ca-d2669de85974/dqc_reference/reference_markers_gtdb.fasta -out GCA_022754405.1_ASM2275440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:17,563] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:17,567] [INFO] Selected 12 target genomes.
[2023-06-13 17:56:17,567] [INFO] Target genome list was writen to GCA_022754405.1_ASM2275440v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:56:17,568] [INFO] Task started: fastANI
[2023-06-13 17:56:17,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d51a7d-49ed-48e0-8743-cabf4ac5bd6f/GCA_022754405.1_ASM2275440v1_genomic.fna.gz --refList GCA_022754405.1_ASM2275440v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022754405.1_ASM2275440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:56:21,186] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:21,190] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:56:21,190] [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_000160875.1	s__Lactobacillus iners	99.1461	86	90	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
--------------------------------------------------------------------------------
[2023-06-13 17:56:21,192] [INFO] GTDB search result was written to GCA_022754405.1_ASM2275440v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:56:21,193] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:56:21,195] [INFO] DFAST_QC result json was written to GCA_022754405.1_ASM2275440v1_genomic.fna/dqc_result.json
[2023-06-13 17:56:21,195] [INFO] DFAST_QC completed!
[2023-06-13 17:56:21,195] [INFO] Total running time: 0h0m19s