tmp/3407079133035171875/tmp_hsp1/941510883324284880/blastp.sh: line 99: 13762 Killed

Expected Behavior

assign taxonomy to Metagenome contigs, and the database is created from krakenuniq bacterial database.

Current Behavior

tmp/3407079133035171875/tmp_hsp1/941510883324284880/blastp.sh: line 99: 13762 Killed $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMPPATH/pref$STEP" $PREFILTER_PAR -s "$SENS" Error: Prefilter died Error: Search step died Error: First search died

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders. mmseqs createdb ~/04.db/krakenuniq/library/nt-bacteria-dustmasked.fna nt-bacteria-dustmasked --dbtype 2 mmseqs createtaxdb nt-bacteria-dustmasked tmp --ncbi-tax-dump ~/04.db/krakenuniq/taxonomy --tax-mapping-file ~/04.db/krakenuniq/library/nt-bacteria.fna.map mmseqs createdb BIN_REASSEMBLY/reassembled_bins/bin.18.strict.fa test mmseqs taxonomy --threads 16 test ~/04.db/mmseqs/taxonomy/nt-bacteria-dustmasked test_res tmp --search-type 3

MMseqs Output (for bugs)

Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output. Header split mode 0 Chain overlapping alignments 0 Merge query 1 Search type 3 Exhaustive search mode false Filter results during exhaustive search 0 Strand selection 1 LCA search mode false Disk space limit 0 MPI runner Force restart with latest tmp false Remove temporary files false

Accel. 2bLCA cannot be used with nucl-nucl taxonomy, using top-hit instead search test /public/home/bh2022044/04.db/mmseqs/taxonomy/nt-bacteria-dustmasked tmp/3407079133035171875/first tmp/3407079133035171875/tmp_hsp1 --alignment-mode 1 -e 1 --max-rejected 5 --max-accept 30 --threads 16 -s 2 --mask 0 --spaced-kmer-mode 1 --min-length 30 --max-length 32734 --orf-start-mode 1 --search-type 3

prefilter tmp/3407079133035171875/tmp_hsp1/941510883324284880/query_seqs_split tmp/3407079133035171875/tmp_hsp1/941510883324284880/target_seqs_split tmp/3407079133035171875/tmp_hsp1/941510883324284880/search/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 15 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 10000 --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 1 --mask 0 --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 16 --compressed 0 -v 3 -s 2.0

Query database size: 960 type: Nucleotide Estimated memory consumption: 1T Target database size: 26422067 type: Nucleotide Index table k-mer threshold: 0 at k-mer size 15 Index table: counting k-mers [> ] 0.00% 1 eta -

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters):
Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
Operating system and version:

system:linux Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 56 On-line CPU(s) list: 0-55 Thread(s) per core: 1 Core(s) per socket: 28 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 106 Model name: Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz

soedinglab / MMseqs2