[2023-06-08 14:46:25,961] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:25,964] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:25,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference
[2023-06-08 14:46:28,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:28,127] [INFO] Task started: Prodigal
[2023-06-08 14:46:28,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d9d4639-e3b9-4b1a-80fc-8138753796b5/GCA_947486545.1_RH-9nov16-95_genomic.fna.gz | prodigal -d GCA_947486545.1_RH-9nov16-95_genomic.fna/cds.fna -a GCA_947486545.1_RH-9nov16-95_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:31,978] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:31,978] [INFO] Task started: HMMsearch
[2023-06-08 14:46:31,978] [INFO] Running command: hmmsearch --tblout GCA_947486545.1_RH-9nov16-95_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/reference_markers.hmm GCA_947486545.1_RH-9nov16-95_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:32,205] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:32,206] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7d9d4639-e3b9-4b1a-80fc-8138753796b5/GCA_947486545.1_RH-9nov16-95_genomic.fna.gz]
[2023-06-08 14:46:32,228] [INFO] Query marker FASTA was written to GCA_947486545.1_RH-9nov16-95_genomic.fna/markers.fasta
[2023-06-08 14:46:32,228] [INFO] Task started: Blastn
[2023-06-08 14:46:32,228] [INFO] Running command: blastn -query GCA_947486545.1_RH-9nov16-95_genomic.fna/markers.fasta -db /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/reference_markers.fasta -out GCA_947486545.1_RH-9nov16-95_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:32,729] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:32,734] [INFO] Selected 15 target genomes.
[2023-06-08 14:46:32,734] [INFO] Target genome list was writen to GCA_947486545.1_RH-9nov16-95_genomic.fna/target_genomes.txt
[2023-06-08 14:46:32,739] [INFO] Task started: fastANI
[2023-06-08 14:46:32,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9d4639-e3b9-4b1a-80fc-8138753796b5/GCA_947486545.1_RH-9nov16-95_genomic.fna.gz --refList GCA_947486545.1_RH-9nov16-95_genomic.fna/target_genomes.txt --output GCA_947486545.1_RH-9nov16-95_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:46:47,799] [INFO] Task succeeded: fastANI
[2023-06-08 14:46:47,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:46:47,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:46:47,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:46:47,803] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:46:47,803] [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
--------------------------------------------------------------------------------
[2023-06-08 14:46:47,813] [INFO] DFAST Taxonomy check result was written to GCA_947486545.1_RH-9nov16-95_genomic.fna/tc_result.tsv
[2023-06-08 14:46:47,814] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:46:47,814] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:46:47,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/checkm_data
[2023-06-08 14:46:47,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:46:47,838] [INFO] Task started: CheckM
[2023-06-08 14:46:47,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947486545.1_RH-9nov16-95_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947486545.1_RH-9nov16-95_genomic.fna/checkm_input GCA_947486545.1_RH-9nov16-95_genomic.fna/checkm_result
[2023-06-08 14:47:06,218] [INFO] Task succeeded: CheckM
[2023-06-08 14:47:06,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:47:06,239] [INFO] ===== Completeness check finished =====
[2023-06-08 14:47:06,240] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:47:06,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947486545.1_RH-9nov16-95_genomic.fna/markers.fasta)
[2023-06-08 14:47:06,240] [INFO] Task started: Blastn
[2023-06-08 14:47:06,240] [INFO] Running command: blastn -query GCA_947486545.1_RH-9nov16-95_genomic.fna/markers.fasta -db /var/lib/cwl/stg68facafb-83f7-45b5-9f5a-e45f8338e3d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_947486545.1_RH-9nov16-95_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:06,714] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:06,719] [INFO] Selected 13 target genomes.
[2023-06-08 14:47:06,719] [INFO] Target genome list was writen to GCA_947486545.1_RH-9nov16-95_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:47:06,728] [INFO] Task started: fastANI
[2023-06-08 14:47:06,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d9d4639-e3b9-4b1a-80fc-8138753796b5/GCA_947486545.1_RH-9nov16-95_genomic.fna.gz --refList GCA_947486545.1_RH-9nov16-95_genomic.fna/target_genomes_gtdb.txt --output GCA_947486545.1_RH-9nov16-95_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:12,942] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:12,947] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:47:12,947] [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_900299345.1	s__UBA11236 sp003455335	77.5103	104	377	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__UBA11236;f__UBA11236;g__UBA11236	95.0	99.85	99.85	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:12,950] [INFO] GTDB search result was written to GCA_947486545.1_RH-9nov16-95_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:12,950] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:12,952] [INFO] DFAST_QC result json was written to GCA_947486545.1_RH-9nov16-95_genomic.fna/dqc_result.json
[2023-06-08 14:47:12,953] [INFO] DFAST_QC completed!
[2023-06-08 14:47:12,953] [INFO] Total running time: 0h0m47s