[2024-01-24 11:18:17,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:17,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:17,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference
[2024-01-24 11:18:19,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:19,087] [INFO] Task started: Prodigal
[2024-01-24 11:18:19,087] [INFO] Running command: gunzip -c /var/lib/cwl/stgaad82d53-f784-40d3-9217-febdb000912f/GCF_900454345.1_51726_A01_genomic.fna.gz | prodigal -d GCF_900454345.1_51726_A01_genomic.fna/cds.fna -a GCF_900454345.1_51726_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:24,689] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:24,690] [INFO] Task started: HMMsearch
[2024-01-24 11:18:24,690] [INFO] Running command: hmmsearch --tblout GCF_900454345.1_51726_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/reference_markers.hmm GCF_900454345.1_51726_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:24,937] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:24,939] [INFO] Found 6/6 markers.
[2024-01-24 11:18:24,961] [INFO] Query marker FASTA was written to GCF_900454345.1_51726_A01_genomic.fna/markers.fasta
[2024-01-24 11:18:24,962] [INFO] Task started: Blastn
[2024-01-24 11:18:24,962] [INFO] Running command: blastn -query GCF_900454345.1_51726_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/reference_markers.fasta -out GCF_900454345.1_51726_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:25,611] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:25,614] [INFO] Selected 16 target genomes.
[2024-01-24 11:18:25,615] [INFO] Target genome list was writen to GCF_900454345.1_51726_A01_genomic.fna/target_genomes.txt
[2024-01-24 11:18:25,634] [INFO] Task started: fastANI
[2024-01-24 11:18:25,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad82d53-f784-40d3-9217-febdb000912f/GCF_900454345.1_51726_A01_genomic.fna.gz --refList GCF_900454345.1_51726_A01_genomic.fna/target_genomes.txt --output GCF_900454345.1_51726_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:34,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:34,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:34,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:34,071] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:18:34,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:34,071] [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
Oligella urethralis	strain=NCTC12964	GCA_900454345.1	90245	90245	type	True	100.0	794	794	95	conclusive
Oligella urethralis	strain=DSM 7531	GCA_000372065.1	90245	90245	type	True	99.9275	748	794	95	conclusive
Oligella ureolytica	strain=FDAARGOS_872	GCA_016028735.1	90244	90244	type	True	79.8778	294	794	95	below_threshold
Oligella ureolytica	strain=NCTC11997	GCA_900454285.1	90244	90244	type	True	79.8219	280	794	95	below_threshold
Oligella ureolytica	strain=DSM 18253	GCA_000373745.1	90244	90244	type	True	79.2521	273	794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:34,072] [INFO] DFAST Taxonomy check result was written to GCF_900454345.1_51726_A01_genomic.fna/tc_result.tsv
[2024-01-24 11:18:34,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:34,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:34,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/checkm_data
[2024-01-24 11:18:34,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:34,098] [INFO] Task started: CheckM
[2024-01-24 11:18:34,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454345.1_51726_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454345.1_51726_A01_genomic.fna/checkm_input GCF_900454345.1_51726_A01_genomic.fna/checkm_result
[2024-01-24 11:18:57,371] [INFO] Task succeeded: CheckM
[2024-01-24 11:18:57,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:18:57,395] [INFO] ===== Completeness check finished =====
[2024-01-24 11:18:57,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:18:57,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454345.1_51726_A01_genomic.fna/markers.fasta)
[2024-01-24 11:18:57,396] [INFO] Task started: Blastn
[2024-01-24 11:18:57,396] [INFO] Running command: blastn -query GCF_900454345.1_51726_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaaf6fd5-eef0-444f-9bf3-01515e33c63d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454345.1_51726_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:58,397] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:58,402] [INFO] Selected 18 target genomes.
[2024-01-24 11:18:58,402] [INFO] Target genome list was writen to GCF_900454345.1_51726_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:18:58,420] [INFO] Task started: fastANI
[2024-01-24 11:18:58,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgaad82d53-f784-40d3-9217-febdb000912f/GCF_900454345.1_51726_A01_genomic.fna.gz --refList GCF_900454345.1_51726_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454345.1_51726_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:06,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:06,349] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:19:06,349] [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_000372065.1	s__Oligella urethralis	99.9275	748	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	98.59	98.11	0.93	0.89	13	conclusive
GCF_000373745.1	s__Oligella ureolytica	79.2324	275	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	99.14	97.93	0.95	0.87	5	-
GCA_012511555.1	s__Oligella sp012511555	78.6052	210	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012511095.1	s__Oligella sp012511095	78.5775	208	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518515.1	s__Oligella sp012518515	78.4793	246	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:19:06,351] [INFO] GTDB search result was written to GCF_900454345.1_51726_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:06,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:06,354] [INFO] DFAST_QC result json was written to GCF_900454345.1_51726_A01_genomic.fna/dqc_result.json
[2024-01-24 11:19:06,354] [INFO] DFAST_QC completed!
[2024-01-24 11:19:06,354] [INFO] Total running time: 0h0m49s