[2024-01-24 12:14:10,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,246] [INFO] DQC Reference Directory: /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference
[2024-01-24 12:14:11,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,674] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4408ace-a1fd-42ba-9183-d3c55bec3543/GCF_022064045.1_ASM2206404v1_genomic.fna.gz | prodigal -d GCF_022064045.1_ASM2206404v1_genomic.fna/cds.fna -a GCF_022064045.1_ASM2206404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:21,630] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:21,630] [INFO] Task started: HMMsearch
[2024-01-24 12:14:21,631] [INFO] Running command: hmmsearch --tblout GCF_022064045.1_ASM2206404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/reference_markers.hmm GCF_022064045.1_ASM2206404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:21,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:21,875] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb4408ace-a1fd-42ba-9183-d3c55bec3543/GCF_022064045.1_ASM2206404v1_genomic.fna.gz]
[2024-01-24 12:14:21,897] [INFO] Query marker FASTA was written to GCF_022064045.1_ASM2206404v1_genomic.fna/markers.fasta
[2024-01-24 12:14:21,898] [INFO] Task started: Blastn
[2024-01-24 12:14:21,898] [INFO] Running command: blastn -query GCF_022064045.1_ASM2206404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/reference_markers.fasta -out GCF_022064045.1_ASM2206404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:22,388] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:22,392] [INFO] Selected 1 target genomes.
[2024-01-24 12:14:22,393] [INFO] Target genome list was writen to GCF_022064045.1_ASM2206404v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:22,395] [INFO] Task started: fastANI
[2024-01-24 12:14:22,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4408ace-a1fd-42ba-9183-d3c55bec3543/GCF_022064045.1_ASM2206404v1_genomic.fna.gz --refList GCF_022064045.1_ASM2206404v1_genomic.fna/target_genomes.txt --output GCF_022064045.1_ASM2206404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:22,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:22,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:22,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:22,877] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:22,878] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 12:14:22,878] [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
--------------------------------------------------------------------------------
[2024-01-24 12:14:22,879] [INFO] DFAST Taxonomy check result was written to GCF_022064045.1_ASM2206404v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:22,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:22,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:22,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/checkm_data
[2024-01-24 12:14:22,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:22,908] [INFO] Task started: CheckM
[2024-01-24 12:14:22,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022064045.1_ASM2206404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022064045.1_ASM2206404v1_genomic.fna/checkm_input GCF_022064045.1_ASM2206404v1_genomic.fna/checkm_result
[2024-01-24 12:14:56,771] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:56,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,796] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:56,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:56,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022064045.1_ASM2206404v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:56,797] [INFO] Task started: Blastn
[2024-01-24 12:14:56,797] [INFO] Running command: blastn -query GCF_022064045.1_ASM2206404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba451932-6467-44eb-a244-4eaf18dd1aaa/dqc_reference/reference_markers_gtdb.fasta -out GCF_022064045.1_ASM2206404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:57,239] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:57,242] [INFO] Selected 2 target genomes.
[2024-01-24 12:14:57,242] [INFO] Target genome list was writen to GCF_022064045.1_ASM2206404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:57,245] [INFO] Task started: fastANI
[2024-01-24 12:14:57,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4408ace-a1fd-42ba-9183-d3c55bec3543/GCF_022064045.1_ASM2206404v1_genomic.fna.gz --refList GCF_022064045.1_ASM2206404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022064045.1_ASM2206404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:57,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:57,909] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:14:57,909] [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
--------------------------------------------------------------------------------
[2024-01-24 12:14:57,910] [INFO] GTDB search result was written to GCF_022064045.1_ASM2206404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:57,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:57,912] [INFO] DFAST_QC result json was written to GCF_022064045.1_ASM2206404v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:57,912] [INFO] DFAST_QC completed!
[2024-01-24 12:14:57,913] [INFO] Total running time: 0h0m48s