[2024-01-24 13:45:59,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:59,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:59,421] [INFO] DQC Reference Directory: /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference
[2024-01-24 13:46:00,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,738] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg9721a931-d15f-4417-a99e-1e10491c3b18/GCF_000196175.1_ASM19617v1_genomic.fna.gz | prodigal -d GCF_000196175.1_ASM19617v1_genomic.fna/cds.fna -a GCF_000196175.1_ASM19617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:11,968] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:11,969] [INFO] Task started: HMMsearch
[2024-01-24 13:46:11,969] [INFO] Running command: hmmsearch --tblout GCF_000196175.1_ASM19617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/reference_markers.hmm GCF_000196175.1_ASM19617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,247] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,290] [INFO] Query marker FASTA was written to GCF_000196175.1_ASM19617v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,291] [INFO] Task started: Blastn
[2024-01-24 13:46:12,291] [INFO] Running command: blastn -query GCF_000196175.1_ASM19617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/reference_markers.fasta -out GCF_000196175.1_ASM19617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:12,868] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:12,872] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:12,873] [INFO] Target genome list was writen to GCF_000196175.1_ASM19617v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:12,897] [INFO] Task started: fastANI
[2024-01-24 13:46:12,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg9721a931-d15f-4417-a99e-1e10491c3b18/GCF_000196175.1_ASM19617v1_genomic.fna.gz --refList GCF_000196175.1_ASM19617v1_genomic.fna/target_genomes.txt --output GCF_000196175.1_ASM19617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:26,830] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:26,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:26,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:26,837] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:26,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:26,838] [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
Bdellovibrio bacteriovorus	strain=HD100	GCA_000196175.1	959	959	suspected-type	True	100.0	1259	1260	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:46:26,840] [INFO] DFAST Taxonomy check result was written to GCF_000196175.1_ASM19617v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:26,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:26,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:26,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/checkm_data
[2024-01-24 13:46:26,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:26,879] [INFO] Task started: CheckM
[2024-01-24 13:46:26,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196175.1_ASM19617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196175.1_ASM19617v1_genomic.fna/checkm_input GCF_000196175.1_ASM19617v1_genomic.fna/checkm_result
[2024-01-24 13:47:05,350] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:05,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:05,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:05,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196175.1_ASM19617v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:05,373] [INFO] Task started: Blastn
[2024-01-24 13:47:05,373] [INFO] Running command: blastn -query GCF_000196175.1_ASM19617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge898c0ce-0788-4e1e-9f32-8b21b6567769/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196175.1_ASM19617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:06,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:06,132] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:06,132] [INFO] Target genome list was writen to GCF_000196175.1_ASM19617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:06,182] [INFO] Task started: fastANI
[2024-01-24 13:47:06,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg9721a931-d15f-4417-a99e-1e10491c3b18/GCF_000196175.1_ASM19617v1_genomic.fna.gz --refList GCF_000196175.1_ASM19617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196175.1_ASM19617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:14,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:14,474] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:14,475] [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_000196175.1	s__Bdellovibrio bacteriovorus	100.0	1258	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	98.95	98.95	0.97	0.97	2	conclusive
GCF_002208115.1	s__Bdellovibrio bacteriovorus_C	90.9063	1134	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317895.1	s__Bdellovibrio bacteriovorus_F	90.3164	1138	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592755.1	s__Bdellovibrio bacteriovorus_E	79.1706	436	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592745.1	s__Bdellovibrio bacteriovorus_B	79.1057	433	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874625.1	s__Bdellovibrio sp006874625	78.8882	322	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000786105.1	s__Bdellovibrio sp000786105	78.6161	372	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745015.1	s__Bdellovibrio sp017745015	78.3986	263	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592735.1	s__Bdellovibrio bacteriovorus_D	78.3634	273	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360185.1	s__Bdellovibrio sp013360185	78.2987	283	1260	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,477] [INFO] GTDB search result was written to GCF_000196175.1_ASM19617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:14,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:14,481] [INFO] DFAST_QC result json was written to GCF_000196175.1_ASM19617v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:14,481] [INFO] DFAST_QC completed!
[2024-01-24 13:47:14,481] [INFO] Total running time: 0h1m15s