[2024-01-25 17:45:50,684] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:50,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:50,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference
[2024-01-25 17:45:51,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:51,803] [INFO] Task started: Prodigal
[2024-01-25 17:45:51,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg95a30dc3-bfb8-4d76-a163-18c2f4d6e88f/GCF_027116575.1_ASM2711657v1_genomic.fna.gz | prodigal -d GCF_027116575.1_ASM2711657v1_genomic.fna/cds.fna -a GCF_027116575.1_ASM2711657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:57,697] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:57,698] [INFO] Task started: HMMsearch
[2024-01-25 17:45:57,698] [INFO] Running command: hmmsearch --tblout GCF_027116575.1_ASM2711657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/reference_markers.hmm GCF_027116575.1_ASM2711657v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:57,894] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:57,895] [INFO] Found 6/6 markers.
[2024-01-25 17:45:57,914] [INFO] Query marker FASTA was written to GCF_027116575.1_ASM2711657v1_genomic.fna/markers.fasta
[2024-01-25 17:45:57,914] [INFO] Task started: Blastn
[2024-01-25 17:45:57,914] [INFO] Running command: blastn -query GCF_027116575.1_ASM2711657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/reference_markers.fasta -out GCF_027116575.1_ASM2711657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:58,583] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:58,586] [INFO] Selected 34 target genomes.
[2024-01-25 17:45:58,586] [INFO] Target genome list was writen to GCF_027116575.1_ASM2711657v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:58,628] [INFO] Task started: fastANI
[2024-01-25 17:45:58,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg95a30dc3-bfb8-4d76-a163-18c2f4d6e88f/GCF_027116575.1_ASM2711657v1_genomic.fna.gz --refList GCF_027116575.1_ASM2711657v1_genomic.fna/target_genomes.txt --output GCF_027116575.1_ASM2711657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:25,477] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:25,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:25,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:25,482] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:25,482] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:25,482] [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
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	75.9854	53	761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:25,483] [INFO] DFAST Taxonomy check result was written to GCF_027116575.1_ASM2711657v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:25,483] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:25,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:25,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/checkm_data
[2024-01-25 17:46:25,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:25,510] [INFO] Task started: CheckM
[2024-01-25 17:46:25,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027116575.1_ASM2711657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027116575.1_ASM2711657v1_genomic.fna/checkm_input GCF_027116575.1_ASM2711657v1_genomic.fna/checkm_result
[2024-01-25 17:46:47,725] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:47,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:47,744] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:47,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:47,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027116575.1_ASM2711657v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:47,744] [INFO] Task started: Blastn
[2024-01-25 17:46:47,745] [INFO] Running command: blastn -query GCF_027116575.1_ASM2711657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce16f1e8-cce2-4ebf-b921-6b1fdf6d9c29/dqc_reference/reference_markers_gtdb.fasta -out GCF_027116575.1_ASM2711657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:48,882] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:48,885] [INFO] Selected 18 target genomes.
[2024-01-25 17:46:48,885] [INFO] Target genome list was writen to GCF_027116575.1_ASM2711657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:48,913] [INFO] Task started: fastANI
[2024-01-25 17:46:48,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg95a30dc3-bfb8-4d76-a163-18c2f4d6e88f/GCF_027116575.1_ASM2711657v1_genomic.fna.gz --refList GCF_027116575.1_ASM2711657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027116575.1_ASM2711657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:01,500] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:01,505] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:01,505] [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_900760095.1	s__Oxalobacter sp900760095	96.3576	617	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000158475.2	s__Oxalobacter formigenes_B	80.6962	475	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	99.93	99.93	0.99	0.99	2	-
GCF_002127965.1	s__Oxalobacter formigenes	78.899	313	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	99.83	99.22	0.99	0.98	6	-
GCA_905202055.1	s__Oxalobacter sp905202055	78.2378	290	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384065.1	s__Oxalobacter sp018384065	77.0714	83	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524145.1	s__Oxalobacter sp017524145	76.7073	67	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012512465.1	s__Oxalobacter sp012512465	76.5064	55	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:01,507] [INFO] GTDB search result was written to GCF_027116575.1_ASM2711657v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:01,507] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:01,509] [INFO] DFAST_QC result json was written to GCF_027116575.1_ASM2711657v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:01,509] [INFO] DFAST_QC completed!
[2024-01-25 17:47:01,509] [INFO] Total running time: 0h1m11s