[2023-06-16 20:59:39,324] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:59:39,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:59:39,326] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference
[2023-06-16 20:59:40,455] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:59:40,455] [INFO] Task started: Prodigal
[2023-06-16 20:59:40,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg716d36c5-37bd-4639-9a0b-368657406781/GCA_003155385.1_20120700_E3M_genomic.fna.gz | prodigal -d GCA_003155385.1_20120700_E3M_genomic.fna/cds.fna -a GCA_003155385.1_20120700_E3M_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:59:43,316] [INFO] Task succeeded: Prodigal
[2023-06-16 20:59:43,317] [INFO] Task started: HMMsearch
[2023-06-16 20:59:43,317] [INFO] Running command: hmmsearch --tblout GCA_003155385.1_20120700_E3M_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/reference_markers.hmm GCA_003155385.1_20120700_E3M_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:59:43,493] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:59:43,494] [INFO] Found 6/6 markers.
[2023-06-16 20:59:43,506] [INFO] Query marker FASTA was written to GCA_003155385.1_20120700_E3M_genomic.fna/markers.fasta
[2023-06-16 20:59:43,506] [INFO] Task started: Blastn
[2023-06-16 20:59:43,506] [INFO] Running command: blastn -query GCA_003155385.1_20120700_E3M_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/reference_markers.fasta -out GCA_003155385.1_20120700_E3M_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:59:44,020] [INFO] Task succeeded: Blastn
[2023-06-16 20:59:44,044] [INFO] Selected 16 target genomes.
[2023-06-16 20:59:44,044] [INFO] Target genome list was writen to GCA_003155385.1_20120700_E3M_genomic.fna/target_genomes.txt
[2023-06-16 20:59:44,049] [INFO] Task started: fastANI
[2023-06-16 20:59:44,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg716d36c5-37bd-4639-9a0b-368657406781/GCA_003155385.1_20120700_E3M_genomic.fna.gz --refList GCA_003155385.1_20120700_E3M_genomic.fna/target_genomes.txt --output GCA_003155385.1_20120700_E3M_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:59:54,281] [INFO] Task succeeded: fastANI
[2023-06-16 20:59:54,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:59:54,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:59:54,283] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:59:54,283] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 20:59:54,283] [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
--------------------------------------------------------------------------------
[2023-06-16 20:59:54,284] [INFO] DFAST Taxonomy check result was written to GCA_003155385.1_20120700_E3M_genomic.fna/tc_result.tsv
[2023-06-16 20:59:54,285] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:59:54,285] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:59:54,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/checkm_data
[2023-06-16 20:59:54,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:59:54,300] [INFO] Task started: CheckM
[2023-06-16 20:59:54,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003155385.1_20120700_E3M_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003155385.1_20120700_E3M_genomic.fna/checkm_input GCA_003155385.1_20120700_E3M_genomic.fna/checkm_result
[2023-06-16 21:00:09,023] [INFO] Task succeeded: CheckM
[2023-06-16 21:00:09,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.94%
Contamintation: 3.08%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2023-06-16 21:00:09,041] [INFO] ===== Completeness check finished =====
[2023-06-16 21:00:09,041] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:00:09,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003155385.1_20120700_E3M_genomic.fna/markers.fasta)
[2023-06-16 21:00:09,042] [INFO] Task started: Blastn
[2023-06-16 21:00:09,042] [INFO] Running command: blastn -query GCA_003155385.1_20120700_E3M_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbe7809d-6d44-4883-b1b2-8813e264d815/dqc_reference/reference_markers_gtdb.fasta -out GCA_003155385.1_20120700_E3M_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:00:09,748] [INFO] Task succeeded: Blastn
[2023-06-16 21:00:09,751] [INFO] Selected 19 target genomes.
[2023-06-16 21:00:09,751] [INFO] Target genome list was writen to GCA_003155385.1_20120700_E3M_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:00:09,770] [INFO] Task started: fastANI
[2023-06-16 21:00:09,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg716d36c5-37bd-4639-9a0b-368657406781/GCA_003155385.1_20120700_E3M_genomic.fna.gz --refList GCA_003155385.1_20120700_E3M_genomic.fna/target_genomes_gtdb.txt --output GCA_003155385.1_20120700_E3M_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:00:13,656] [INFO] Task succeeded: fastANI
[2023-06-16 21:00:13,659] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:00:13,659] [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_003155695.1	s__UBA8515 sp003155695	99.9073	248	266	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.96	99.96	0.96	0.96	2	conclusive
--------------------------------------------------------------------------------
[2023-06-16 21:00:13,660] [INFO] GTDB search result was written to GCA_003155385.1_20120700_E3M_genomic.fna/result_gtdb.tsv
[2023-06-16 21:00:13,661] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:00:13,663] [INFO] DFAST_QC result json was written to GCA_003155385.1_20120700_E3M_genomic.fna/dqc_result.json
[2023-06-16 21:00:13,663] [INFO] DFAST_QC completed!
[2023-06-16 21:00:13,663] [INFO] Total running time: 0h0m34s