[2024-01-24 13:13:25,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:25,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:25,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference
[2024-01-24 13:13:27,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,122] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg39628174-42a4-4721-aac9-2486f32a246d/GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/cds.fna -a GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:39,720] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:39,720] [INFO] Task started: HMMsearch
[2024-01-24 13:13:39,720] [INFO] Running command: hmmsearch --tblout GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/reference_markers.hmm GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,022] [INFO] Found 6/6 markers.
[2024-01-24 13:13:40,070] [INFO] Query marker FASTA was written to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:40,071] [INFO] Task started: Blastn
[2024-01-24 13:13:40,071] [INFO] Running command: blastn -query GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/reference_markers.fasta -out GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:40,717] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:40,720] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:40,720] [INFO] Target genome list was writen to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:40,788] [INFO] Task started: fastANI
[2024-01-24 13:13:40,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg39628174-42a4-4721-aac9-2486f32a246d/GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna.gz --refList GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:49,151] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:49,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:49,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:49,154] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:49,155] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:13:49,155] [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 13:13:49,161] [INFO] DFAST Taxonomy check result was written to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:49,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:49,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:49,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/checkm_data
[2024-01-24 13:13:49,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:49,215] [INFO] Task started: CheckM
[2024-01-24 13:13:49,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/checkm_input GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:31,039] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:31,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:31,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:31,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:31,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:31,064] [INFO] Task started: Blastn
[2024-01-24 13:14:31,064] [INFO] Running command: blastn -query GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f921128-4926-4744-9380-a5966d63e08d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:32,155] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:32,159] [INFO] Selected 29 target genomes.
[2024-01-24 13:14:32,160] [INFO] Target genome list was writen to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:32,288] [INFO] Task started: fastANI
[2024-01-24 13:14:32,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg39628174-42a4-4721-aac9-2486f32a246d/GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna.gz --refList GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:43,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:43,671] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:14:43,671] [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_011390155.1	s__JAABSW01 sp011390155	77.2485	158	1362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Tindalliaceae;g__JAABSW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:43,673] [INFO] GTDB search result was written to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:43,674] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:43,675] [INFO] DFAST_QC result json was written to GCF_900182905.1_IMG-taxon_2706794923_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:43,676] [INFO] DFAST_QC completed!
[2024-01-24 13:14:43,676] [INFO] Total running time: 0h1m18s