[2023-06-28 15:16:30,915] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:16:30,918] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:16:30,918] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference
[2023-06-28 15:16:32,085] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:16:32,086] [INFO] Task started: Prodigal
[2023-06-28 15:16:32,087] [INFO] Running command: gunzip -c /var/lib/cwl/stga70a94d1-3d04-408e-a809-5dcbbf67ae3d/GCA_020059085.1_ASM2005908v1_genomic.fna.gz | prodigal -d GCA_020059085.1_ASM2005908v1_genomic.fna/cds.fna -a GCA_020059085.1_ASM2005908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:16:38,110] [INFO] Task succeeded: Prodigal
[2023-06-28 15:16:38,111] [INFO] Task started: HMMsearch
[2023-06-28 15:16:38,111] [INFO] Running command: hmmsearch --tblout GCA_020059085.1_ASM2005908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/reference_markers.hmm GCA_020059085.1_ASM2005908v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:16:38,315] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:16:38,317] [INFO] Found 6/6 markers.
[2023-06-28 15:16:38,342] [INFO] Query marker FASTA was written to GCA_020059085.1_ASM2005908v1_genomic.fna/markers.fasta
[2023-06-28 15:16:38,343] [INFO] Task started: Blastn
[2023-06-28 15:16:38,343] [INFO] Running command: blastn -query GCA_020059085.1_ASM2005908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/reference_markers.fasta -out GCA_020059085.1_ASM2005908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:16:38,930] [INFO] Task succeeded: Blastn
[2023-06-28 15:16:38,934] [INFO] Selected 39 target genomes.
[2023-06-28 15:16:38,934] [INFO] Target genome list was writen to GCA_020059085.1_ASM2005908v1_genomic.fna/target_genomes.txt
[2023-06-28 15:16:38,936] [INFO] Task started: fastANI
[2023-06-28 15:16:38,936] [INFO] Running command: fastANI --query /var/lib/cwl/stga70a94d1-3d04-408e-a809-5dcbbf67ae3d/GCA_020059085.1_ASM2005908v1_genomic.fna.gz --refList GCA_020059085.1_ASM2005908v1_genomic.fna/target_genomes.txt --output GCA_020059085.1_ASM2005908v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:17:08,835] [INFO] Task succeeded: fastANI
[2023-06-28 15:17:08,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:17:08,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:17:08,837] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:17:08,837] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 15:17:08,837] [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
--------------------------------------------------------------------------------
[2023-06-28 15:17:08,839] [INFO] DFAST Taxonomy check result was written to GCA_020059085.1_ASM2005908v1_genomic.fna/tc_result.tsv
[2023-06-28 15:17:08,840] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:17:08,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:17:08,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/checkm_data
[2023-06-28 15:17:08,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:17:08,871] [INFO] Task started: CheckM
[2023-06-28 15:17:08,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020059085.1_ASM2005908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020059085.1_ASM2005908v1_genomic.fna/checkm_input GCA_020059085.1_ASM2005908v1_genomic.fna/checkm_result
[2023-06-28 15:17:33,164] [INFO] Task succeeded: CheckM
[2023-06-28 15:17:33,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 34.38%
Strain heterogeneity: 41.67%
--------------------------------------------------------------------------------
[2023-06-28 15:17:33,190] [INFO] ===== Completeness check finished =====
[2023-06-28 15:17:33,191] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:17:33,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020059085.1_ASM2005908v1_genomic.fna/markers.fasta)
[2023-06-28 15:17:33,191] [INFO] Task started: Blastn
[2023-06-28 15:17:33,191] [INFO] Running command: blastn -query GCA_020059085.1_ASM2005908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2622a57-86fe-49d0-90b3-bdd19c5a412a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020059085.1_ASM2005908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:17:33,976] [INFO] Task succeeded: Blastn
[2023-06-28 15:17:33,980] [INFO] Selected 48 target genomes.
[2023-06-28 15:17:33,981] [INFO] Target genome list was writen to GCA_020059085.1_ASM2005908v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:17:33,996] [INFO] Task started: fastANI
[2023-06-28 15:17:33,996] [INFO] Running command: fastANI --query /var/lib/cwl/stga70a94d1-3d04-408e-a809-5dcbbf67ae3d/GCA_020059085.1_ASM2005908v1_genomic.fna.gz --refList GCA_020059085.1_ASM2005908v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020059085.1_ASM2005908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:18:00,682] [INFO] Task succeeded: fastANI
[2023-06-28 15:18:00,685] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:18:00,685] [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_013297865.1	s__JAAFIP01 sp013297865	76.404	56	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFIP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:18:00,687] [INFO] GTDB search result was written to GCA_020059085.1_ASM2005908v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:18:00,687] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:18:00,689] [INFO] DFAST_QC result json was written to GCA_020059085.1_ASM2005908v1_genomic.fna/dqc_result.json
[2023-06-28 15:18:00,689] [INFO] DFAST_QC completed!
[2023-06-28 15:18:00,690] [INFO] Total running time: 0h1m30s