[2023-06-13 10:10:44,214] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:44,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:44,218] [INFO] DQC Reference Directory: /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference
[2023-06-13 10:10:47,159] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:47,160] [INFO] Task started: Prodigal
[2023-06-13 10:10:47,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg15a15b9b-4c0a-40ee-aa04-d0209b255d6d/GCA_947448205.1_Jr-11may16-165_genomic.fna.gz | prodigal -d GCA_947448205.1_Jr-11may16-165_genomic.fna/cds.fna -a GCA_947448205.1_Jr-11may16-165_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:51,646] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:51,655] [INFO] Task started: HMMsearch
[2023-06-13 10:10:51,655] [INFO] Running command: hmmsearch --tblout GCA_947448205.1_Jr-11may16-165_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/reference_markers.hmm GCA_947448205.1_Jr-11may16-165_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:52,022] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:52,024] [INFO] Found 6/6 markers.
[2023-06-13 10:10:52,077] [INFO] Query marker FASTA was written to GCA_947448205.1_Jr-11may16-165_genomic.fna/markers.fasta
[2023-06-13 10:10:52,078] [INFO] Task started: Blastn
[2023-06-13 10:10:52,078] [INFO] Running command: blastn -query GCA_947448205.1_Jr-11may16-165_genomic.fna/markers.fasta -db /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/reference_markers.fasta -out GCA_947448205.1_Jr-11may16-165_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:52,794] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:52,798] [INFO] Selected 16 target genomes.
[2023-06-13 10:10:52,798] [INFO] Target genome list was writen to GCA_947448205.1_Jr-11may16-165_genomic.fna/target_genomes.txt
[2023-06-13 10:10:52,803] [INFO] Task started: fastANI
[2023-06-13 10:10:52,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a15b9b-4c0a-40ee-aa04-d0209b255d6d/GCA_947448205.1_Jr-11may16-165_genomic.fna.gz --refList GCA_947448205.1_Jr-11may16-165_genomic.fna/target_genomes.txt --output GCA_947448205.1_Jr-11may16-165_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:00,563] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:00,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:00,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:00,568] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:00,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:11:00,569] [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
Bacteriovorax stolpii	strain=DSM 12778	GCA_004362635.1	960	960	type	True	76.7133	134	788	95	below_threshold
Bacteriovorax stolpii	strain=DSM 12778	GCA_002872415.1	960	960	type	True	76.6892	131	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:11:00,571] [INFO] DFAST Taxonomy check result was written to GCA_947448205.1_Jr-11may16-165_genomic.fna/tc_result.tsv
[2023-06-13 10:11:00,572] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:00,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:00,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/checkm_data
[2023-06-13 10:11:00,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:00,614] [INFO] Task started: CheckM
[2023-06-13 10:11:00,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947448205.1_Jr-11may16-165_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947448205.1_Jr-11may16-165_genomic.fna/checkm_input GCA_947448205.1_Jr-11may16-165_genomic.fna/checkm_result
[2023-06-13 10:11:22,694] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:22,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:22,715] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:22,716] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:22,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947448205.1_Jr-11may16-165_genomic.fna/markers.fasta)
[2023-06-13 10:11:22,717] [INFO] Task started: Blastn
[2023-06-13 10:11:22,717] [INFO] Running command: blastn -query GCA_947448205.1_Jr-11may16-165_genomic.fna/markers.fasta -db /var/lib/cwl/stga946e11f-6baa-4fd7-adcd-b7fa2dff145c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947448205.1_Jr-11may16-165_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:23,536] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:23,541] [INFO] Selected 16 target genomes.
[2023-06-13 10:11:23,542] [INFO] Target genome list was writen to GCA_947448205.1_Jr-11may16-165_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:23,554] [INFO] Task started: fastANI
[2023-06-13 10:11:23,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a15b9b-4c0a-40ee-aa04-d0209b255d6d/GCA_947448205.1_Jr-11may16-165_genomic.fna.gz --refList GCA_947448205.1_Jr-11may16-165_genomic.fna/target_genomes_gtdb.txt --output GCA_947448205.1_Jr-11may16-165_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:32,681] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:32,696] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:11:32,696] [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_014377485.1	s__Bacteriovorax sp014377485	77.8208	285	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018060625.1	s__Bacteriovorax sp018060625	77.7296	218	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141065.1	s__Bacteriovorax sp013141065	77.5177	173	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440825.1	s__Bacteriovorax sp002440825	77.1167	163	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428265.1	s__Bacteriovorax sp002428265	76.8668	169	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872415.1	s__Bacteriovorax stolpii	76.7053	130	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	99.34	98.67	0.98	0.97	3	-
GCA_014378525.1	s__Bacteriovorax sp014378525	76.7042	148	788	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:11:32,698] [INFO] GTDB search result was written to GCA_947448205.1_Jr-11may16-165_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:32,699] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:32,701] [INFO] DFAST_QC result json was written to GCA_947448205.1_Jr-11may16-165_genomic.fna/dqc_result.json
[2023-06-13 10:11:32,702] [INFO] DFAST_QC completed!
[2023-06-13 10:11:32,702] [INFO] Total running time: 0h0m48s