[2024-01-24 13:17:15,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,284] [INFO] DQC Reference Directory: /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference
[2024-01-24 13:17:16,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,715] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,715] [INFO] Running command: gunzip -c /var/lib/cwl/stge92613dc-1571-4adb-a104-8bfd762e17f6/GCF_004362635.1_ASM436263v1_genomic.fna.gz | prodigal -d GCF_004362635.1_ASM436263v1_genomic.fna/cds.fna -a GCF_004362635.1_ASM436263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:25,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:25,450] [INFO] Task started: HMMsearch
[2024-01-24 13:17:25,450] [INFO] Running command: hmmsearch --tblout GCF_004362635.1_ASM436263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/reference_markers.hmm GCF_004362635.1_ASM436263v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:25,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:25,758] [INFO] Found 6/6 markers.
[2024-01-24 13:17:25,794] [INFO] Query marker FASTA was written to GCF_004362635.1_ASM436263v1_genomic.fna/markers.fasta
[2024-01-24 13:17:25,794] [INFO] Task started: Blastn
[2024-01-24 13:17:25,794] [INFO] Running command: blastn -query GCF_004362635.1_ASM436263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/reference_markers.fasta -out GCF_004362635.1_ASM436263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:26,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:26,427] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:26,428] [INFO] Target genome list was writen to GCF_004362635.1_ASM436263v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:26,434] [INFO] Task started: fastANI
[2024-01-24 13:17:26,434] [INFO] Running command: fastANI --query /var/lib/cwl/stge92613dc-1571-4adb-a104-8bfd762e17f6/GCF_004362635.1_ASM436263v1_genomic.fna.gz --refList GCF_004362635.1_ASM436263v1_genomic.fna/target_genomes.txt --output GCF_004362635.1_ASM436263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:36,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:36,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:36,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:36,807] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:36,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:36,807] [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	100.0	1260	1261	95	conclusive
Bacteriovorax stolpii	strain=DSM 12778	GCA_002872415.1	960	960	type	True	99.9989	1260	1261	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:36,809] [INFO] DFAST Taxonomy check result was written to GCF_004362635.1_ASM436263v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:36,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:36,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:36,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/checkm_data
[2024-01-24 13:17:36,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:36,850] [INFO] Task started: CheckM
[2024-01-24 13:17:36,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362635.1_ASM436263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362635.1_ASM436263v1_genomic.fna/checkm_input GCF_004362635.1_ASM436263v1_genomic.fna/checkm_result
[2024-01-24 13:18:08,059] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:08,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:08,089] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:08,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:08,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362635.1_ASM436263v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:08,091] [INFO] Task started: Blastn
[2024-01-24 13:18:08,091] [INFO] Running command: blastn -query GCF_004362635.1_ASM436263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga965e0d9-fade-4511-9bb3-dc7745e59918/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362635.1_ASM436263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,928] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:08,928] [INFO] Target genome list was writen to GCF_004362635.1_ASM436263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:08,951] [INFO] Task started: fastANI
[2024-01-24 13:18:08,951] [INFO] Running command: fastANI --query /var/lib/cwl/stge92613dc-1571-4adb-a104-8bfd762e17f6/GCF_004362635.1_ASM436263v1_genomic.fna.gz --refList GCF_004362635.1_ASM436263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362635.1_ASM436263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:17,092] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:17,104] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:17,105] [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
GCF_002872415.1	s__Bacteriovorax stolpii	99.9989	1260	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	99.34	98.67	0.98	0.97	3	conclusive
GCA_002428265.1	s__Bacteriovorax sp002428265	79.5405	515	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378525.1	s__Bacteriovorax sp014378525	78.8804	495	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376445.1	s__Bacteriovorax sp014376445	78.3741	396	1261	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	78.0585	234	1261	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	77.9222	230	1261	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	77.2322	132	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377485.1	s__Bacteriovorax sp014377485	77.1957	214	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Bacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447755.1	s__BSW11-IV sp000447755	76.7394	60	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__BSW11-IV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447795.1	s__DB6-IX sp000447795	75.7751	56	1261	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:17,107] [INFO] GTDB search result was written to GCF_004362635.1_ASM436263v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:17,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:17,110] [INFO] DFAST_QC result json was written to GCF_004362635.1_ASM436263v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:17,110] [INFO] DFAST_QC completed!
[2024-01-24 13:18:17,110] [INFO] Total running time: 0h1m2s