[2023-06-13 12:28:08,263] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:28:08,265] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:28:08,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference
[2023-06-13 12:28:09,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:28:09,648] [INFO] Task started: Prodigal
[2023-06-13 12:28:09,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dd1808b-74de-4502-84c5-5c5b4f18e498/GCA_022599895.1_ASM2259989v1_genomic.fna.gz | prodigal -d GCA_022599895.1_ASM2259989v1_genomic.fna/cds.fna -a GCA_022599895.1_ASM2259989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:28:14,178] [INFO] Task succeeded: Prodigal
[2023-06-13 12:28:14,179] [INFO] Task started: HMMsearch
[2023-06-13 12:28:14,179] [INFO] Running command: hmmsearch --tblout GCA_022599895.1_ASM2259989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/reference_markers.hmm GCA_022599895.1_ASM2259989v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:28:14,408] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:28:14,410] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1dd1808b-74de-4502-84c5-5c5b4f18e498/GCA_022599895.1_ASM2259989v1_genomic.fna.gz]
[2023-06-13 12:28:14,436] [INFO] Query marker FASTA was written to GCA_022599895.1_ASM2259989v1_genomic.fna/markers.fasta
[2023-06-13 12:28:14,436] [INFO] Task started: Blastn
[2023-06-13 12:28:14,436] [INFO] Running command: blastn -query GCA_022599895.1_ASM2259989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/reference_markers.fasta -out GCA_022599895.1_ASM2259989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:15,078] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:15,084] [INFO] Selected 26 target genomes.
[2023-06-13 12:28:15,084] [INFO] Target genome list was writen to GCA_022599895.1_ASM2259989v1_genomic.fna/target_genomes.txt
[2023-06-13 12:28:15,092] [INFO] Task started: fastANI
[2023-06-13 12:28:15,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd1808b-74de-4502-84c5-5c5b4f18e498/GCA_022599895.1_ASM2259989v1_genomic.fna.gz --refList GCA_022599895.1_ASM2259989v1_genomic.fna/target_genomes.txt --output GCA_022599895.1_ASM2259989v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:28:29,440] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:29,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:28:29,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:28:29,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:28:29,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 12:28:29,443] [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
--------------------------------------------------------------------------------
[2023-06-13 12:28:29,456] [INFO] DFAST Taxonomy check result was written to GCA_022599895.1_ASM2259989v1_genomic.fna/tc_result.tsv
[2023-06-13 12:28:29,457] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:28:29,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:28:29,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/checkm_data
[2023-06-13 12:28:29,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:28:29,490] [INFO] Task started: CheckM
[2023-06-13 12:28:29,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022599895.1_ASM2259989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022599895.1_ASM2259989v1_genomic.fna/checkm_input GCA_022599895.1_ASM2259989v1_genomic.fna/checkm_result
[2023-06-13 12:28:50,107] [INFO] Task succeeded: CheckM
[2023-06-13 12:28:50,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 12:28:50,139] [INFO] ===== Completeness check finished =====
[2023-06-13 12:28:50,140] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:28:50,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022599895.1_ASM2259989v1_genomic.fna/markers.fasta)
[2023-06-13 12:28:50,140] [INFO] Task started: Blastn
[2023-06-13 12:28:50,141] [INFO] Running command: blastn -query GCA_022599895.1_ASM2259989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be95d10-d62b-4330-a992-e48c4f75669a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022599895.1_ASM2259989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:51,131] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:51,137] [INFO] Selected 19 target genomes.
[2023-06-13 12:28:51,137] [INFO] Target genome list was writen to GCA_022599895.1_ASM2259989v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:28:51,179] [INFO] Task started: fastANI
[2023-06-13 12:28:51,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd1808b-74de-4502-84c5-5c5b4f18e498/GCA_022599895.1_ASM2259989v1_genomic.fna.gz --refList GCA_022599895.1_ASM2259989v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022599895.1_ASM2259989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:29:01,198] [INFO] Task succeeded: fastANI
[2023-06-13 12:29:01,206] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:29:01,206] [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_001438145.1	s__UBA9145 sp001438145	96.9517	474	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.16	96.74	0.82	0.76	25	conclusive
GCA_018401885.1	s__UBA9145 sp018401885	79.8357	332	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.27	98.07	0.94	0.93	3	-
GCA_017853205.1	s__UBA9145 sp003482475	79.7189	323	587	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.11	98.58	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-13 12:29:01,208] [INFO] GTDB search result was written to GCA_022599895.1_ASM2259989v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:29:01,210] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:29:01,212] [INFO] DFAST_QC result json was written to GCA_022599895.1_ASM2259989v1_genomic.fna/dqc_result.json
[2023-06-13 12:29:01,212] [INFO] DFAST_QC completed!
[2023-06-13 12:29:01,213] [INFO] Total running time: 0h0m53s