[2023-06-04 17:30:43,989] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:30:43,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:30:43,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference
[2023-06-04 17:30:45,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:30:45,545] [INFO] Task started: Prodigal
[2023-06-04 17:30:45,545] [INFO] Running command: gunzip -c /var/lib/cwl/stgcac5407b-2600-479b-96c6-1532f251cc34/GCA_004294865.1_ASM429486v1_genomic.fna.gz | prodigal -d GCA_004294865.1_ASM429486v1_genomic.fna/cds.fna -a GCA_004294865.1_ASM429486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:30:48,014] [INFO] Task succeeded: Prodigal
[2023-06-04 17:30:48,015] [INFO] Task started: HMMsearch
[2023-06-04 17:30:48,015] [INFO] Running command: hmmsearch --tblout GCA_004294865.1_ASM429486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/reference_markers.hmm GCA_004294865.1_ASM429486v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:30:48,237] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:30:48,238] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcac5407b-2600-479b-96c6-1532f251cc34/GCA_004294865.1_ASM429486v1_genomic.fna.gz]
[2023-06-04 17:30:48,261] [INFO] Query marker FASTA was written to GCA_004294865.1_ASM429486v1_genomic.fna/markers.fasta
[2023-06-04 17:30:48,262] [INFO] Task started: Blastn
[2023-06-04 17:30:48,262] [INFO] Running command: blastn -query GCA_004294865.1_ASM429486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/reference_markers.fasta -out GCA_004294865.1_ASM429486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:49,896] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:49,902] [INFO] Selected 22 target genomes.
[2023-06-04 17:30:49,902] [INFO] Target genome list was writen to GCA_004294865.1_ASM429486v1_genomic.fna/target_genomes.txt
[2023-06-04 17:30:55,291] [INFO] Task started: fastANI
[2023-06-04 17:30:55,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac5407b-2600-479b-96c6-1532f251cc34/GCA_004294865.1_ASM429486v1_genomic.fna.gz --refList GCA_004294865.1_ASM429486v1_genomic.fna/target_genomes.txt --output GCA_004294865.1_ASM429486v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:31:08,649] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:08,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:31:08,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:31:08,654] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 17:31:08,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 17:31:08,654] [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
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	99.2607	320	365	95	conclusive
--------------------------------------------------------------------------------
[2023-06-04 17:31:08,656] [INFO] DFAST Taxonomy check result was written to GCA_004294865.1_ASM429486v1_genomic.fna/tc_result.tsv
[2023-06-04 17:31:08,657] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:31:08,657] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:31:08,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/checkm_data
[2023-06-04 17:31:08,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:31:08,684] [INFO] Task started: CheckM
[2023-06-04 17:31:08,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004294865.1_ASM429486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004294865.1_ASM429486v1_genomic.fna/checkm_input GCA_004294865.1_ASM429486v1_genomic.fna/checkm_result
[2023-06-04 17:31:24,502] [INFO] Task succeeded: CheckM
[2023-06-04 17:31:24,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:31:24,526] [INFO] ===== Completeness check finished =====
[2023-06-04 17:31:24,526] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:31:24,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004294865.1_ASM429486v1_genomic.fna/markers.fasta)
[2023-06-04 17:31:24,527] [INFO] Task started: Blastn
[2023-06-04 17:31:24,527] [INFO] Running command: blastn -query GCA_004294865.1_ASM429486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3249cd07-95ef-4387-8a58-42a42e4e2d11/dqc_reference/reference_markers_gtdb.fasta -out GCA_004294865.1_ASM429486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:25,318] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:25,323] [INFO] Selected 23 target genomes.
[2023-06-04 17:31:25,324] [INFO] Target genome list was writen to GCA_004294865.1_ASM429486v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:31:25,798] [INFO] Task started: fastANI
[2023-06-04 17:31:25,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac5407b-2600-479b-96c6-1532f251cc34/GCA_004294865.1_ASM429486v1_genomic.fna.gz --refList GCA_004294865.1_ASM429486v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004294865.1_ASM429486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:31:36,144] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:36,152] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:31:36,152] [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_900107485.1	s__Proteiniborus ethanoligenes	99.2607	320	365	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002376545.1	s__Proteiniborus sp002376545	77.9919	120	365	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	99.93	99.93	0.97	0.97	2	-
GCF_900095305.1	s__Proteiniborus sp900095305	77.8353	119	365	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:31:36,154] [INFO] GTDB search result was written to GCA_004294865.1_ASM429486v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:31:36,155] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:31:36,157] [INFO] DFAST_QC result json was written to GCA_004294865.1_ASM429486v1_genomic.fna/dqc_result.json
[2023-06-04 17:31:36,157] [INFO] DFAST_QC completed!
[2023-06-04 17:31:36,158] [INFO] Total running time: 0h0m52s