[2023-06-05 08:30:51,629] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:30:51,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:30:51,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference
[2023-06-05 08:30:53,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:30:53,930] [INFO] Task started: Prodigal
[2023-06-05 08:30:53,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg3860347f-3f3e-489e-9856-e9d08538d3ce/GCA_004562645.1_ASM456264v1_genomic.fna.gz | prodigal -d GCA_004562645.1_ASM456264v1_genomic.fna/cds.fna -a GCA_004562645.1_ASM456264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:30:55,769] [INFO] Task succeeded: Prodigal
[2023-06-05 08:30:55,770] [INFO] Task started: HMMsearch
[2023-06-05 08:30:55,771] [INFO] Running command: hmmsearch --tblout GCA_004562645.1_ASM456264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/reference_markers.hmm GCA_004562645.1_ASM456264v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:30:55,967] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:30:55,969] [INFO] Found 6/6 markers.
[2023-06-05 08:30:55,985] [INFO] Query marker FASTA was written to GCA_004562645.1_ASM456264v1_genomic.fna/markers.fasta
[2023-06-05 08:30:55,985] [INFO] Task started: Blastn
[2023-06-05 08:30:55,986] [INFO] Running command: blastn -query GCA_004562645.1_ASM456264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/reference_markers.fasta -out GCA_004562645.1_ASM456264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:30:58,697] [INFO] Task succeeded: Blastn
[2023-06-05 08:30:58,702] [INFO] Selected 15 target genomes.
[2023-06-05 08:30:58,703] [INFO] Target genome list was writen to GCA_004562645.1_ASM456264v1_genomic.fna/target_genomes.txt
[2023-06-05 08:30:58,720] [INFO] Task started: fastANI
[2023-06-05 08:30:58,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg3860347f-3f3e-489e-9856-e9d08538d3ce/GCA_004562645.1_ASM456264v1_genomic.fna.gz --refList GCA_004562645.1_ASM456264v1_genomic.fna/target_genomes.txt --output GCA_004562645.1_ASM456264v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:31:06,787] [INFO] Task succeeded: fastANI
[2023-06-05 08:31:06,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:31:06,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:31:06,790] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:31:06,790] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:31:06,790] [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
--------------------------------------------------------------------------------
[2023-06-05 08:31:06,792] [INFO] DFAST Taxonomy check result was written to GCA_004562645.1_ASM456264v1_genomic.fna/tc_result.tsv
[2023-06-05 08:31:06,793] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:31:06,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:31:06,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/checkm_data
[2023-06-05 08:31:06,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:31:06,867] [INFO] Task started: CheckM
[2023-06-05 08:31:06,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004562645.1_ASM456264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004562645.1_ASM456264v1_genomic.fna/checkm_input GCA_004562645.1_ASM456264v1_genomic.fna/checkm_result
[2023-06-05 08:31:20,680] [INFO] Task succeeded: CheckM
[2023-06-05 08:31:20,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:31:20,704] [INFO] ===== Completeness check finished =====
[2023-06-05 08:31:20,705] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:31:20,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004562645.1_ASM456264v1_genomic.fna/markers.fasta)
[2023-06-05 08:31:20,706] [INFO] Task started: Blastn
[2023-06-05 08:31:20,706] [INFO] Running command: blastn -query GCA_004562645.1_ASM456264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9021e7c-5d35-4701-aeb6-160e81fdc1e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_004562645.1_ASM456264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:31:21,509] [INFO] Task succeeded: Blastn
[2023-06-05 08:31:21,514] [INFO] Selected 16 target genomes.
[2023-06-05 08:31:21,514] [INFO] Target genome list was writen to GCA_004562645.1_ASM456264v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:31:21,528] [INFO] Task started: fastANI
[2023-06-05 08:31:21,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg3860347f-3f3e-489e-9856-e9d08538d3ce/GCA_004562645.1_ASM456264v1_genomic.fna.gz --refList GCA_004562645.1_ASM456264v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004562645.1_ASM456264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:31:24,295] [INFO] Task succeeded: fastANI
[2023-06-05 08:31:24,306] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:31:24,306] [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
GCA_004561445.1	s__UBA2834 sp004561445	97.2304	202	226	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016290315.1	s__UBA2834 sp016290315	77.5003	51	226	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017514805.1	s__UBA2834 sp017514805	77.236	51	226	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371895.1	s__UBA2834 sp002371895	77.2356	64	226	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437945.1	s__UBA2834 sp017437945	77.2281	58	226	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__UBA2834	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:31:24,308] [INFO] GTDB search result was written to GCA_004562645.1_ASM456264v1_genomic.fna/result_gtdb.tsv
[2023-06-05 08:31:24,309] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:31:24,312] [INFO] DFAST_QC result json was written to GCA_004562645.1_ASM456264v1_genomic.fna/dqc_result.json
[2023-06-05 08:31:24,313] [INFO] DFAST_QC completed!
[2023-06-05 08:31:24,313] [INFO] Total running time: 0h0m33s