[2024-01-25 19:04:20,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:20,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:20,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference
[2024-01-25 19:04:21,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:21,747] [INFO] Task started: Prodigal
[2024-01-25 19:04:21,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg90b4d653-d81f-4b7f-b534-961079c4e65f/GCF_000525915.1_Bcampestris_genomic.fna.gz | prodigal -d GCF_000525915.1_Bcampestris_genomic.fna/cds.fna -a GCF_000525915.1_Bcampestris_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:25,995] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:25,996] [INFO] Task started: HMMsearch
[2024-01-25 19:04:25,996] [INFO] Running command: hmmsearch --tblout GCF_000525915.1_Bcampestris_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/reference_markers.hmm GCF_000525915.1_Bcampestris_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:26,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:26,198] [INFO] Found 6/6 markers.
[2024-01-25 19:04:26,220] [INFO] Query marker FASTA was written to GCF_000525915.1_Bcampestris_genomic.fna/markers.fasta
[2024-01-25 19:04:26,220] [INFO] Task started: Blastn
[2024-01-25 19:04:26,220] [INFO] Running command: blastn -query GCF_000525915.1_Bcampestris_genomic.fna/markers.fasta -db /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/reference_markers.fasta -out GCF_000525915.1_Bcampestris_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:26,772] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:26,775] [INFO] Selected 24 target genomes.
[2024-01-25 19:04:26,775] [INFO] Target genome list was writen to GCF_000525915.1_Bcampestris_genomic.fna/target_genomes.txt
[2024-01-25 19:04:26,792] [INFO] Task started: fastANI
[2024-01-25 19:04:26,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b4d653-d81f-4b7f-b534-961079c4e65f/GCF_000525915.1_Bcampestris_genomic.fna.gz --refList GCF_000525915.1_Bcampestris_genomic.fna/target_genomes.txt --output GCF_000525915.1_Bcampestris_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:36,509] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:36,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:36,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:36,514] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:36,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:36,514] [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
Brochothrix campestris	strain=FSL F6-1037	GCA_000525915.1	2757	2757	type	True	100.0	735	740	95	conclusive
Brochothrix thermosphacta	strain=DSM 20171	GCA_000620985.1	2756	2756	type	True	79.6653	267	740	95	below_threshold
Brochothrix thermosphacta	strain=DSM 20171	GCA_001715655.1	2756	2756	type	True	79.6412	266	740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:36,515] [INFO] DFAST Taxonomy check result was written to GCF_000525915.1_Bcampestris_genomic.fna/tc_result.tsv
[2024-01-25 19:04:36,517] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:36,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:36,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/checkm_data
[2024-01-25 19:04:36,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:36,544] [INFO] Task started: CheckM
[2024-01-25 19:04:36,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000525915.1_Bcampestris_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000525915.1_Bcampestris_genomic.fna/checkm_input GCF_000525915.1_Bcampestris_genomic.fna/checkm_result
[2024-01-25 19:04:55,114] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:55,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:55,133] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:55,133] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:55,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000525915.1_Bcampestris_genomic.fna/markers.fasta)
[2024-01-25 19:04:55,133] [INFO] Task started: Blastn
[2024-01-25 19:04:55,134] [INFO] Running command: blastn -query GCF_000525915.1_Bcampestris_genomic.fna/markers.fasta -db /var/lib/cwl/stg4742f291-1cfe-43af-a072-f26fcbbaf17d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000525915.1_Bcampestris_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:55,875] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:55,878] [INFO] Selected 25 target genomes.
[2024-01-25 19:04:55,879] [INFO] Target genome list was writen to GCF_000525915.1_Bcampestris_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:55,898] [INFO] Task started: fastANI
[2024-01-25 19:04:55,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b4d653-d81f-4b7f-b534-961079c4e65f/GCF_000525915.1_Bcampestris_genomic.fna.gz --refList GCF_000525915.1_Bcampestris_genomic.fna/target_genomes_gtdb.txt --output GCF_000525915.1_Bcampestris_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:08,043] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:08,047] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:08,047] [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_000525915.1	s__Brochothrix campestris	100.0	735	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Brochothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000620985.1	s__Brochothrix thermosphacta	79.678	266	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Brochothrix	95.0	99.06	98.76	0.94	0.90	27	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:08,048] [INFO] GTDB search result was written to GCF_000525915.1_Bcampestris_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:08,048] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:08,050] [INFO] DFAST_QC result json was written to GCF_000525915.1_Bcampestris_genomic.fna/dqc_result.json
[2024-01-25 19:05:08,050] [INFO] DFAST_QC completed!
[2024-01-25 19:05:08,051] [INFO] Total running time: 0h0m47s