[2023-06-28 21:14:26,357] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:14:26,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:14:26,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference
[2023-06-28 21:14:27,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:14:27,713] [INFO] Task started: Prodigal
[2023-06-28 21:14:27,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg10adbd33-82b3-4d99-b80d-bb09369a8ac1/GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:14:36,384] [INFO] Task succeeded: Prodigal
[2023-06-28 21:14:36,385] [INFO] Task started: HMMsearch
[2023-06-28 21:14:36,385] [INFO] Running command: hmmsearch --tblout GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/reference_markers.hmm GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:14:36,663] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:14:36,664] [INFO] Found 6/6 markers.
[2023-06-28 21:14:36,700] [INFO] Query marker FASTA was written to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 21:14:36,701] [INFO] Task started: Blastn
[2023-06-28 21:14:36,701] [INFO] Running command: blastn -query GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/reference_markers.fasta -out GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:14:37,393] [INFO] Task succeeded: Blastn
[2023-06-28 21:14:37,396] [INFO] Selected 34 target genomes.
[2023-06-28 21:14:37,397] [INFO] Target genome list was writen to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 21:14:37,416] [INFO] Task started: fastANI
[2023-06-28 21:14:37,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg10adbd33-82b3-4d99-b80d-bb09369a8ac1/GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:14:59,751] [INFO] Task succeeded: fastANI
[2023-06-28 21:14:59,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:14:59,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:14:59,755] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:14:59,755] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:14:59,755] [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 21:14:59,757] [INFO] DFAST Taxonomy check result was written to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 21:14:59,758] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:14:59,758] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:14:59,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/checkm_data
[2023-06-28 21:14:59,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:14:59,803] [INFO] Task started: CheckM
[2023-06-28 21:14:59,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 21:15:30,795] [INFO] Task succeeded: CheckM
[2023-06-28 21:15:30,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 21:15:30,819] [INFO] ===== Completeness check finished =====
[2023-06-28 21:15:30,820] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:15:30,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 21:15:30,821] [INFO] Task started: Blastn
[2023-06-28 21:15:30,821] [INFO] Running command: blastn -query GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3f8372-f2d6-4d8a-9860-00686e9a456c/dqc_reference/reference_markers_gtdb.fasta -out GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:15:31,857] [INFO] Task succeeded: Blastn
[2023-06-28 21:15:31,863] [INFO] Selected 35 target genomes.
[2023-06-28 21:15:31,863] [INFO] Target genome list was writen to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:15:31,911] [INFO] Task started: fastANI
[2023-06-28 21:15:31,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg10adbd33-82b3-4d99-b80d-bb09369a8ac1/GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:15:53,097] [INFO] Task succeeded: fastANI
[2023-06-28 21:15:53,100] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:15:53,100] [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_006212045.1	s__PZPK01 sp006212045	76.3153	105	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__PZPK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:15:53,102] [INFO] GTDB search result was written to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 21:15:53,103] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:15:53,105] [INFO] DFAST_QC result json was written to GCA_913020045.1_SRR5469033_bin.54_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 21:15:53,105] [INFO] DFAST_QC completed!
[2023-06-28 21:15:53,105] [INFO] Total running time: 0h1m27s