[2024-01-24 13:09:33,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference
[2024-01-24 13:09:34,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:34,883] [INFO] Task started: Prodigal
[2024-01-24 13:09:34,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf0a9330-4f76-44d1-978a-b5de3a42c893/GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/cds.fna -a GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:41,261] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:41,262] [INFO] Task started: HMMsearch
[2024-01-24 13:09:41,262] [INFO] Running command: hmmsearch --tblout GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/reference_markers.hmm GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:41,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:41,480] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbf0a9330-4f76-44d1-978a-b5de3a42c893/GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna.gz]
[2024-01-24 13:09:41,513] [INFO] Query marker FASTA was written to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:41,514] [INFO] Task started: Blastn
[2024-01-24 13:09:41,514] [INFO] Running command: blastn -query GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/reference_markers.fasta -out GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:42,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:42,058] [INFO] Selected 6 target genomes.
[2024-01-24 13:09:42,059] [INFO] Target genome list was writen to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:42,067] [INFO] Task started: fastANI
[2024-01-24 13:09:42,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf0a9330-4f76-44d1-978a-b5de3a42c893/GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna.gz --refList GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:45,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:45,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:45,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:45,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:09:45,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:09:45,427] [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 13:09:45,429] [INFO] DFAST Taxonomy check result was written to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:09:45,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:45,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:45,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/checkm_data
[2024-01-24 13:09:45,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:45,450] [INFO] Task started: CheckM
[2024-01-24 13:09:45,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/checkm_input GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:04,820] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:04,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:04,837] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:04,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:04,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:04,838] [INFO] Task started: Blastn
[2024-01-24 13:10:04,838] [INFO] Running command: blastn -query GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg93e1a736-6bf6-4ad4-8392-fdaf6ab69fcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:05,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:05,244] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:05,244] [INFO] Target genome list was writen to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:05,250] [INFO] Task started: fastANI
[2024-01-24 13:10:05,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf0a9330-4f76-44d1-978a-b5de3a42c893/GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna.gz --refList GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:06,885] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:06,888] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:06,888] [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_900176435.1	s__Picrophilus oshimae	100.0	508	508	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Picrophilus	95.0	98.91	98.91	0.95	0.95	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:10:06,889] [INFO] GTDB search result was written to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:06,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:06,892] [INFO] DFAST_QC result json was written to GCF_900176435.1_IMG-taxon_2579779151_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:10:06,892] [INFO] DFAST_QC completed!
[2024-01-24 13:10:06,892] [INFO] Total running time: 0h0m33s