[2023-06-08 18:24:30,546] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:24:30,551] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:24:30,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference
[2023-06-08 18:24:32,910] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:24:32,911] [INFO] Task started: Prodigal
[2023-06-08 18:24:32,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc288266-81f8-4cc6-b680-db9383e625e1/GCA_947581845.1_3300027893_57.fasta_genomic.fna.gz | prodigal -d GCA_947581845.1_3300027893_57.fasta_genomic.fna/cds.fna -a GCA_947581845.1_3300027893_57.fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:24:37,877] [INFO] Task succeeded: Prodigal
[2023-06-08 18:24:37,877] [INFO] Task started: HMMsearch
[2023-06-08 18:24:37,878] [INFO] Running command: hmmsearch --tblout GCA_947581845.1_3300027893_57.fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/reference_markers.hmm GCA_947581845.1_3300027893_57.fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:24:38,099] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:24:38,101] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbc288266-81f8-4cc6-b680-db9383e625e1/GCA_947581845.1_3300027893_57.fasta_genomic.fna.gz]
[2023-06-08 18:24:38,134] [INFO] Query marker FASTA was written to GCA_947581845.1_3300027893_57.fasta_genomic.fna/markers.fasta
[2023-06-08 18:24:38,135] [INFO] Task started: Blastn
[2023-06-08 18:24:38,135] [INFO] Running command: blastn -query GCA_947581845.1_3300027893_57.fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/reference_markers.fasta -out GCA_947581845.1_3300027893_57.fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:24:38,629] [INFO] Task succeeded: Blastn
[2023-06-08 18:24:38,633] [INFO] Selected 20 target genomes.
[2023-06-08 18:24:38,634] [INFO] Target genome list was writen to GCA_947581845.1_3300027893_57.fasta_genomic.fna/target_genomes.txt
[2023-06-08 18:24:38,639] [INFO] Task started: fastANI
[2023-06-08 18:24:38,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc288266-81f8-4cc6-b680-db9383e625e1/GCA_947581845.1_3300027893_57.fasta_genomic.fna.gz --refList GCA_947581845.1_3300027893_57.fasta_genomic.fna/target_genomes.txt --output GCA_947581845.1_3300027893_57.fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:24:52,408] [INFO] Task succeeded: fastANI
[2023-06-08 18:24:52,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:24:52,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:24:52,412] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:24:52,412] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 18:24:52,412] [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 18:24:52,415] [INFO] DFAST Taxonomy check result was written to GCA_947581845.1_3300027893_57.fasta_genomic.fna/tc_result.tsv
[2023-06-08 18:24:52,416] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:24:52,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:24:52,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/checkm_data
[2023-06-08 18:24:52,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:24:52,447] [INFO] Task started: CheckM
[2023-06-08 18:24:52,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947581845.1_3300027893_57.fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947581845.1_3300027893_57.fasta_genomic.fna/checkm_input GCA_947581845.1_3300027893_57.fasta_genomic.fna/checkm_result
[2023-06-08 18:25:13,760] [INFO] Task succeeded: CheckM
[2023-06-08 18:25:13,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:25:13,781] [INFO] ===== Completeness check finished =====
[2023-06-08 18:25:13,781] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:25:13,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947581845.1_3300027893_57.fasta_genomic.fna/markers.fasta)
[2023-06-08 18:25:13,782] [INFO] Task started: Blastn
[2023-06-08 18:25:13,782] [INFO] Running command: blastn -query GCA_947581845.1_3300027893_57.fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b8f2bd9-94bb-4a3e-8e30-b157d35070b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947581845.1_3300027893_57.fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:14,314] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:14,318] [INFO] Selected 17 target genomes.
[2023-06-08 18:25:14,319] [INFO] Target genome list was writen to GCA_947581845.1_3300027893_57.fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:25:14,358] [INFO] Task started: fastANI
[2023-06-08 18:25:14,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc288266-81f8-4cc6-b680-db9383e625e1/GCA_947581845.1_3300027893_57.fasta_genomic.fna.gz --refList GCA_947581845.1_3300027893_57.fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_947581845.1_3300027893_57.fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:25:23,072] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:23,089] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 18:25:23,089] [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_011774835.1	s__KS3-K002 sp011774835	77.0755	149	586	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__KS3-K002;g__KS3-K002	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 18:25:23,093] [INFO] GTDB search result was written to GCA_947581845.1_3300027893_57.fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 18:25:23,093] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:25:23,097] [INFO] DFAST_QC result json was written to GCA_947581845.1_3300027893_57.fasta_genomic.fna/dqc_result.json
[2023-06-08 18:25:23,097] [INFO] DFAST_QC completed!
[2023-06-08 18:25:23,097] [INFO] Total running time: 0h0m53s