[2024-01-24 13:17:15,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference
[2024-01-24 13:17:17,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,086] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,086] [INFO] Running command: gunzip -c /var/lib/cwl/stgf72dd92b-c593-41fe-8366-159590429160/GCF_019047805.1_ASM1904780v1_genomic.fna.gz | prodigal -d GCF_019047805.1_ASM1904780v1_genomic.fna/cds.fna -a GCF_019047805.1_ASM1904780v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:26,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:26,134] [INFO] Task started: HMMsearch
[2024-01-24 13:17:26,135] [INFO] Running command: hmmsearch --tblout GCF_019047805.1_ASM1904780v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/reference_markers.hmm GCF_019047805.1_ASM1904780v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:26,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:26,382] [INFO] Found 6/6 markers.
[2024-01-24 13:17:26,410] [INFO] Query marker FASTA was written to GCF_019047805.1_ASM1904780v1_genomic.fna/markers.fasta
[2024-01-24 13:17:26,410] [INFO] Task started: Blastn
[2024-01-24 13:17:26,411] [INFO] Running command: blastn -query GCF_019047805.1_ASM1904780v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/reference_markers.fasta -out GCF_019047805.1_ASM1904780v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:27,640] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:27,646] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:27,646] [INFO] Target genome list was writen to GCF_019047805.1_ASM1904780v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:27,650] [INFO] Task started: fastANI
[2024-01-24 13:17:27,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgf72dd92b-c593-41fe-8366-159590429160/GCF_019047805.1_ASM1904780v1_genomic.fna.gz --refList GCF_019047805.1_ASM1904780v1_genomic.fna/target_genomes.txt --output GCF_019047805.1_ASM1904780v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:33,447] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:33,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:33,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:33,457] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:33,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:33,458] [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
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	100.0	960	960	95	conclusive
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	99.9997	959	960	95	conclusive
Corynebacterium xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	87.434	727	960	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	80.5304	467	960	95	below_threshold
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	79.404	282	960	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	79.3434	338	960	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	78.5687	267	960	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	78.2097	199	960	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.8688	234	960	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	77.8671	197	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:33,460] [INFO] DFAST Taxonomy check result was written to GCF_019047805.1_ASM1904780v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:33,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:33,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:33,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/checkm_data
[2024-01-24 13:17:33,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:33,493] [INFO] Task started: CheckM
[2024-01-24 13:17:33,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019047805.1_ASM1904780v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019047805.1_ASM1904780v1_genomic.fna/checkm_input GCF_019047805.1_ASM1904780v1_genomic.fna/checkm_result
[2024-01-24 13:18:09,485] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:09,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,502] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:09,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:09,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019047805.1_ASM1904780v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:09,503] [INFO] Task started: Blastn
[2024-01-24 13:18:09,503] [INFO] Running command: blastn -query GCF_019047805.1_ASM1904780v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8f46f2-4ac6-4ac2-8d34-b5889ace94a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_019047805.1_ASM1904780v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:11,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:11,102] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:11,102] [INFO] Target genome list was writen to GCF_019047805.1_ASM1904780v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:11,108] [INFO] Task started: fastANI
[2024-01-24 13:18:11,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgf72dd92b-c593-41fe-8366-159590429160/GCF_019047805.1_ASM1904780v1_genomic.fna.gz --refList GCF_019047805.1_ASM1904780v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019047805.1_ASM1904780v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:15,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,691] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:15,692] [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_017876455.1	s__Corynebacterium freneyi	99.9997	959	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	conclusive
GCF_001056295.1	s__Corynebacterium halotolerans_A	87.6356	770	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837295.1	s__Corynebacterium sp012837295	87.5818	584	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552415.1	s__Corynebacterium xerosis	87.434	727	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	95.54	0.95	0.90	8	-
GCA_012838715.1	s__Corynebacterium sp012838715	84.0995	426	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	80.5708	466	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209905.1	s__Corynebacterium sp019209905	79.0186	235	960	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,698] [INFO] GTDB search result was written to GCF_019047805.1_ASM1904780v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:15,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:15,702] [INFO] DFAST_QC result json was written to GCF_019047805.1_ASM1904780v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:15,702] [INFO] DFAST_QC completed!
[2024-01-24 13:18:15,702] [INFO] Total running time: 0h0m60s