Can not allocate entries memory in IndexTable::initMemory #5
Description
Hello
I encountered an issue while running the annotate module. Below are the details:
Command Used:
$ transannot annotate trinity_transDecDB Pfam-A_DB eggNOG_DB Swiss-Prot_DB transannot_trinity_transDec_out.tsv tmp
Runtime Output:
MMseqs Version: 4.0.0
Sensitivity 4
Simplified output false
Don't linclust for the redundancy reduction false
Remove temporary files false
Compressed 0
Coverage threshold 0
Seq. id. threshold 0.3
Threads 20
Verbosity 3
omit
prefilter tmp/clu_rep eggNOG_DB tmp/search_tmp/2569736640230882328/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 5.7 -k 5 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 20 --compressed 0 -v 3
Query database size: 30503 type: Aminoacid
Estimated memory consumption: 1G
Target database size: 349750 type: Profile
Index table k-mer threshold: 82 at k-mer size 5
Index table: counting k-mers
[=================================================================] 100.00% 349.75K 1m 1s 768ms
Index table: Masked residues: 0
Can not allocate entries memory in IndexTable::initMemory
Error: Prefilter died
Error: second sequence-profile search died'
System Information:
Hardware: Intel Core i7-12700K, 128 GB RAM, GPU: RTX3060 (12 GB)
Environment: Windows 10 with WSL2 running Ubuntu 24.04.1, Conda 25.1.1 TransAnnot Version: 4.0.0
Installation Details:
I installed TransAnnot using the following commands:
mamba create -n transannot -y
conda activate transannot
mamba install bioconda::transannot -y
conda update transannot
Additional Context:
The input file (trinity_transdecoder.pep) used before conversion via createquerydb is approximately 20 MB in size. During execution, Task Manager shows that memory usage is only about 15% of the total available memory(128GB).
I would greatly appreciate any guidance or suggestions on how to resolve this issue.
Best