[2023-06-13 12:39:43,990] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:39:43,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:39:43,994] [INFO] DQC Reference Directory: /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference
[2023-06-13 12:39:45,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:39:45,352] [INFO] Task started: Prodigal
[2023-06-13 12:39:45,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ee72908-c5f5-407a-a20e-b987a2cf2206/GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna.gz | prodigal -d GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/cds.fna -a GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:39:53,068] [INFO] Task succeeded: Prodigal
[2023-06-13 12:39:53,069] [INFO] Task started: HMMsearch
[2023-06-13 12:39:53,069] [INFO] Running command: hmmsearch --tblout GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/reference_markers.hmm GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:39:53,361] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:39:53,362] [INFO] Found 6/6 markers.
[2023-06-13 12:39:53,390] [INFO] Query marker FASTA was written to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/markers.fasta
[2023-06-13 12:39:53,391] [INFO] Task started: Blastn
[2023-06-13 12:39:53,391] [INFO] Running command: blastn -query GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/reference_markers.fasta -out GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:39:54,076] [INFO] Task succeeded: Blastn
[2023-06-13 12:39:54,080] [INFO] Selected 35 target genomes.
[2023-06-13 12:39:54,080] [INFO] Target genome list was writen to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/target_genomes.txt
[2023-06-13 12:39:54,092] [INFO] Task started: fastANI
[2023-06-13 12:39:54,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ee72908-c5f5-407a-a20e-b987a2cf2206/GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna.gz --refList GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/target_genomes.txt --output GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:40:14,416] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:14,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:40:14,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:40:14,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:40:14,419] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 12:40:14,419] [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 12:40:14,424] [INFO] DFAST Taxonomy check result was written to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/tc_result.tsv
[2023-06-13 12:40:14,425] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:40:14,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:40:14,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/checkm_data
[2023-06-13 12:40:14,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:40:14,472] [INFO] Task started: CheckM
[2023-06-13 12:40:14,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/checkm_input GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/checkm_result
[2023-06-13 12:40:42,828] [INFO] Task succeeded: CheckM
[2023-06-13 12:40:42,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 12:40:42,852] [INFO] ===== Completeness check finished =====
[2023-06-13 12:40:42,853] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:40:42,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/markers.fasta)
[2023-06-13 12:40:42,853] [INFO] Task started: Blastn
[2023-06-13 12:40:42,854] [INFO] Running command: blastn -query GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea345799-6c99-4d59-a66e-f919616d5e67/dqc_reference/reference_markers_gtdb.fasta -out GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:40:43,893] [INFO] Task succeeded: Blastn
[2023-06-13 12:40:43,899] [INFO] Selected 15 target genomes.
[2023-06-13 12:40:43,899] [INFO] Target genome list was writen to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:40:43,908] [INFO] Task started: fastANI
[2023-06-13 12:40:43,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ee72908-c5f5-407a-a20e-b987a2cf2206/GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna.gz --refList GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:40:52,523] [INFO] Task succeeded: fastANI
[2023-06-13 12:40:52,532] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 12:40:52,532] [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_009886205.1	s__UBA4421 sp009886205	99.2357	773	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.44	96.05	0.88	0.79	9	conclusive
GCA_002336645.1	s__UBA4421 sp002336645	83.7369	576	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182095.1	s__UBA4421 sp905182095	81.5444	511	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182905.1	s__UBA4421 sp002390555	79.3666	412	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.65	99.65	0.88	0.88	2	-
GCA_009936775.1	s__UBA4421 sp009936775	76.002	63	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704225.1	s__UBA4421 sp002704225	75.8185	61	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-13 12:40:52,534] [INFO] GTDB search result was written to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:40:52,534] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:40:52,537] [INFO] DFAST_QC result json was written to GCA_938082455.1_S4_Bin_METABAT_316_1_genomic.fna/dqc_result.json
[2023-06-13 12:40:52,537] [INFO] DFAST_QC completed!
[2023-06-13 12:40:52,537] [INFO] Total running time: 0h1m9s