[2024-01-24 12:06:18,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:18,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:18,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference
[2024-01-24 12:06:20,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,041] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c9cad6b-49c4-44a5-afe7-d301663f65e9/GCF_014672835.1_ASM1467283v1_genomic.fna.gz | prodigal -d GCF_014672835.1_ASM1467283v1_genomic.fna/cds.fna -a GCF_014672835.1_ASM1467283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,665] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,666] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,666] [INFO] Running command: hmmsearch --tblout GCF_014672835.1_ASM1467283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/reference_markers.hmm GCF_014672835.1_ASM1467283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,930] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,958] [INFO] Query marker FASTA was written to GCF_014672835.1_ASM1467283v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,958] [INFO] Task started: Blastn
[2024-01-24 12:06:26,958] [INFO] Running command: blastn -query GCF_014672835.1_ASM1467283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/reference_markers.fasta -out GCF_014672835.1_ASM1467283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,580] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,586] [INFO] Selected 21 target genomes.
[2024-01-24 12:06:27,586] [INFO] Target genome list was writen to GCF_014672835.1_ASM1467283v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,597] [INFO] Task started: fastANI
[2024-01-24 12:06:27,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9cad6b-49c4-44a5-afe7-d301663f65e9/GCF_014672835.1_ASM1467283v1_genomic.fna.gz --refList GCF_014672835.1_ASM1467283v1_genomic.fna/target_genomes.txt --output GCF_014672835.1_ASM1467283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,879] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:35,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,880] [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
Entomobacter blattae	strain=G55GP	GCA_014672835.1	2762277	2762277	type	True	100.0	895	900	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,882] [INFO] DFAST Taxonomy check result was written to GCF_014672835.1_ASM1467283v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/checkm_data
[2024-01-24 12:06:35,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,919] [INFO] Task started: CheckM
[2024-01-24 12:06:35,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014672835.1_ASM1467283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014672835.1_ASM1467283v1_genomic.fna/checkm_input GCF_014672835.1_ASM1467283v1_genomic.fna/checkm_result
[2024-01-24 12:07:01,384] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:01,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.80%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-24 12:07:01,411] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:01,411] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:01,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014672835.1_ASM1467283v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:01,412] [INFO] Task started: Blastn
[2024-01-24 12:07:01,412] [INFO] Running command: blastn -query GCF_014672835.1_ASM1467283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc9605c-adaf-4323-9cef-3df92f005f32/dqc_reference/reference_markers_gtdb.fasta -out GCF_014672835.1_ASM1467283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:02,389] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:02,394] [INFO] Selected 25 target genomes.
[2024-01-24 12:07:02,394] [INFO] Target genome list was writen to GCF_014672835.1_ASM1467283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:02,414] [INFO] Task started: fastANI
[2024-01-24 12:07:02,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c9cad6b-49c4-44a5-afe7-d301663f65e9/GCF_014672835.1_ASM1467283v1_genomic.fna.gz --refList GCF_014672835.1_ASM1467283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014672835.1_ASM1467283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:11,949] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:11,954] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:11,954] [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_014672835.1	s__Entomobacter blattae	100.0	899	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Entomobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:07:11,956] [INFO] GTDB search result was written to GCF_014672835.1_ASM1467283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:11,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:11,960] [INFO] DFAST_QC result json was written to GCF_014672835.1_ASM1467283v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:11,960] [INFO] DFAST_QC completed!
[2024-01-24 12:07:11,961] [INFO] Total running time: 0h0m53s