[2024-01-24 14:14:20,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference
[2024-01-24 14:14:21,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,674] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e312640-2f34-4f30-9cce-afb051fa4666/GCF_017161265.1_ASM1716126v1_genomic.fna.gz | prodigal -d GCF_017161265.1_ASM1716126v1_genomic.fna/cds.fna -a GCF_017161265.1_ASM1716126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:28,609] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:28,610] [INFO] Task started: HMMsearch
[2024-01-24 14:14:28,610] [INFO] Running command: hmmsearch --tblout GCF_017161265.1_ASM1716126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/reference_markers.hmm GCF_017161265.1_ASM1716126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:28,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:28,832] [INFO] Found 6/6 markers.
[2024-01-24 14:14:28,856] [INFO] Query marker FASTA was written to GCF_017161265.1_ASM1716126v1_genomic.fna/markers.fasta
[2024-01-24 14:14:28,857] [INFO] Task started: Blastn
[2024-01-24 14:14:28,857] [INFO] Running command: blastn -query GCF_017161265.1_ASM1716126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/reference_markers.fasta -out GCF_017161265.1_ASM1716126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:29,538] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:29,542] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:29,542] [INFO] Target genome list was writen to GCF_017161265.1_ASM1716126v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:29,660] [INFO] Task started: fastANI
[2024-01-24 14:14:29,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e312640-2f34-4f30-9cce-afb051fa4666/GCF_017161265.1_ASM1716126v1_genomic.fna.gz --refList GCF_017161265.1_ASM1716126v1_genomic.fna/target_genomes.txt --output GCF_017161265.1_ASM1716126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:36,899] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:36,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:36,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:36,906] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:36,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:36,906] [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
Treponema medium	strain=ATCC 700293	GCA_017161265.1	58231	58231	type	True	100.0	906	907	95	conclusive
Treponema medium	strain=ATCC 700293	GCA_000413035.1	58231	58231	type	True	99.9791	903	907	95	conclusive
Treponema putidum	strain=OMZ 758	GCA_000755145.1	221027	221027	type	True	80.9666	115	907	95	below_threshold
Treponema denticola	strain=ATCC 35405	GCA_000008185.1	158	158	type	True	80.9554	108	907	95	below_threshold
Treponema putidum	strain=ATCC 700334	GCA_007830595.1	221027	221027	type	True	80.357	113	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:36,908] [INFO] DFAST Taxonomy check result was written to GCF_017161265.1_ASM1716126v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:36,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:36,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:36,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/checkm_data
[2024-01-24 14:14:36,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:36,937] [INFO] Task started: CheckM
[2024-01-24 14:14:36,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161265.1_ASM1716126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161265.1_ASM1716126v1_genomic.fna/checkm_input GCF_017161265.1_ASM1716126v1_genomic.fna/checkm_result
[2024-01-24 14:15:02,401] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:02,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:02,418] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:02,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:02,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161265.1_ASM1716126v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:02,419] [INFO] Task started: Blastn
[2024-01-24 14:15:02,419] [INFO] Running command: blastn -query GCF_017161265.1_ASM1716126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be617d3-9922-489b-8ebe-ec5e715402d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161265.1_ASM1716126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:03,202] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:03,207] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:03,207] [INFO] Target genome list was writen to GCF_017161265.1_ASM1716126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:03,213] [INFO] Task started: fastANI
[2024-01-24 14:15:03,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e312640-2f34-4f30-9cce-afb051fa4666/GCF_017161265.1_ASM1716126v1_genomic.fna.gz --refList GCF_017161265.1_ASM1716126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161265.1_ASM1716126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:10,354] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:10,360] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:10,360] [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_017161265.1	s__Treponema medium	100.0	906	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	98.62	97.26	0.99	0.99	3	conclusive
GCF_018336815.1	s__Treponema sp018336815	91.5247	731	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775995.1	s__Treponema sp000775995	90.6867	699	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365865.1	s__Treponema sp010365865	89.923	733	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373565.1	s__Treponema sp905373565	88.1196	460	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412995.1	s__Treponema vincentii	85.1071	629	907	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	97.95	97.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:10,362] [INFO] GTDB search result was written to GCF_017161265.1_ASM1716126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:10,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:10,365] [INFO] DFAST_QC result json was written to GCF_017161265.1_ASM1716126v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:10,365] [INFO] DFAST_QC completed!
[2024-01-24 14:15:10,365] [INFO] Total running time: 0h0m50s