[2024-01-24 12:06:23,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,178] [INFO] DQC Reference Directory: /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference
[2024-01-24 12:06:24,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:24,478] [INFO] Task started: Prodigal
[2024-01-24 12:06:24,479] [INFO] Running command: gunzip -c /var/lib/cwl/stge37650ee-df0f-4f3f-bacd-32642f5bfcf4/GCF_016908855.1_ASM1690885v1_genomic.fna.gz | prodigal -d GCF_016908855.1_ASM1690885v1_genomic.fna/cds.fna -a GCF_016908855.1_ASM1690885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:31,412] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:31,412] [INFO] Task started: HMMsearch
[2024-01-24 12:06:31,412] [INFO] Running command: hmmsearch --tblout GCF_016908855.1_ASM1690885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/reference_markers.hmm GCF_016908855.1_ASM1690885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:31,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:31,667] [INFO] Found 6/6 markers.
[2024-01-24 12:06:31,694] [INFO] Query marker FASTA was written to GCF_016908855.1_ASM1690885v1_genomic.fna/markers.fasta
[2024-01-24 12:06:31,694] [INFO] Task started: Blastn
[2024-01-24 12:06:31,695] [INFO] Running command: blastn -query GCF_016908855.1_ASM1690885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/reference_markers.fasta -out GCF_016908855.1_ASM1690885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:32,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:32,300] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:32,301] [INFO] Target genome list was writen to GCF_016908855.1_ASM1690885v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:32,316] [INFO] Task started: fastANI
[2024-01-24 12:06:32,316] [INFO] Running command: fastANI --query /var/lib/cwl/stge37650ee-df0f-4f3f-bacd-32642f5bfcf4/GCF_016908855.1_ASM1690885v1_genomic.fna.gz --refList GCF_016908855.1_ASM1690885v1_genomic.fna/target_genomes.txt --output GCF_016908855.1_ASM1690885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:46,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:46,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:46,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:46,526] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:46,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:46,526] [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
Scopulibacillus daqui	strain=DSM 28236	GCA_016908855.1	1469162	1469162	type	True	100.0	1032	1036	95	conclusive
Scopulibacillus darangshiensis	strain=DSM 19377	GCA_004341035.1	442528	442528	type	True	76.6957	128	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:46,528] [INFO] DFAST Taxonomy check result was written to GCF_016908855.1_ASM1690885v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:46,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:46,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:46,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/checkm_data
[2024-01-24 12:06:46,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:46,566] [INFO] Task started: CheckM
[2024-01-24 12:06:46,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908855.1_ASM1690885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908855.1_ASM1690885v1_genomic.fna/checkm_input GCF_016908855.1_ASM1690885v1_genomic.fna/checkm_result
[2024-01-24 12:07:12,359] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:12,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,383] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:12,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:12,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908855.1_ASM1690885v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:12,384] [INFO] Task started: Blastn
[2024-01-24 12:07:12,384] [INFO] Running command: blastn -query GCF_016908855.1_ASM1690885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc49ab744-52ba-4fa2-8da9-96b1eae1c182/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908855.1_ASM1690885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:13,216] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:13,219] [INFO] Selected 28 target genomes.
[2024-01-24 12:07:13,220] [INFO] Target genome list was writen to GCF_016908855.1_ASM1690885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:13,259] [INFO] Task started: fastANI
[2024-01-24 12:07:13,260] [INFO] Running command: fastANI --query /var/lib/cwl/stge37650ee-df0f-4f3f-bacd-32642f5bfcf4/GCF_016908855.1_ASM1690885v1_genomic.fna.gz --refList GCF_016908855.1_ASM1690885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908855.1_ASM1690885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:30,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:30,893] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:30,894] [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_016908855.1	s__Scopulibacillus daqui	100.0	1032	1036	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Scopulibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341035.1	s__Scopulibacillus darangshiensis	76.6957	128	1036	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Scopulibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:30,896] [INFO] GTDB search result was written to GCF_016908855.1_ASM1690885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:30,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:30,898] [INFO] DFAST_QC result json was written to GCF_016908855.1_ASM1690885v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:30,898] [INFO] DFAST_QC completed!
[2024-01-24 12:07:30,898] [INFO] Total running time: 0h1m8s