steineggerlab
Error: target createdb died
While running foldseek easy-search I ran into the following error.
##installed foldseek conda install -c conda-forge -c bioconda foldseek
##installed database foldseek databases Alphafold/Proteome afdb tmp
##try to run easysearch foldseek easy-search /home/z76r142/AlphaFold/models/SLA-04_01093-RD/ranked_1.pdb /home/z76r142/condaenv/ 1093.m8 tmpfolder
##easy search results in following error
MMseqs2 was not compiled with zlib support. Cannot read compressed input. Error: target createdb died
Your Environment
foldseek Version: 2.8bd520 MMseqs2 Version: 13.45111
Bioconda is not updated yet. Please download the binaries from: https://github.com/steineggerlab/foldseek/releases/tag/3-915ef7d
Getting the same error without bioconda install.
Distribution: Ubuntu 22.04 LTS
$ [ $(uname -m) = "x86_64" ] && echo "64bit: Yes" || echo "64bit: No" grep -q avx2 /proc/cpuinfo && echo "AVX2: Yes" || echo "AVX2: No" grep -q sse4_1 /proc/cpuinfo && echo "SSE4.1: Yes" || echo "SSE4.1: No" # for very old systems which support neither SSE4.1 or AVX2 grep -q sse2 /proc/cpuinfo && echo "SSE2: Yes" || echo "SSE2: No" 64bit: Yes AVX2: Yes SSE4.1: Yes SSE2: Yes
$ wget https://github.com/steineggerlab/foldseek/releases/download/3-915ef7d/foldseek-linux-avx2.tar.gz
$ tar xvzf foldseek-linux-avx2.tar.gz
$ foldseek/bin/foldseek createdb ~/Downloads/pdbstyle-sel-gs-bib-40-2.08.tgz astral40db createdb /home/user/Downloads/pdbstyle-sel-gs-bib-40-2.08.tgz astral40db
MMseqs Version: 915ef7ddce1bd77080208eff8a434c0985ae7492 Chain name mode 0 Write lookup file 1 Tar Inclusion Regex .* Tar Exclusion Regex ^$ Threads 8 Verbosity 3
Output file: astral40db MMseqs2 was not compiled with zlib support. Cannot read compressed input.
Bioconda should be up to date now. Can you try if that version works? I have to investigate what’s wrong with the precompiled binaries.
Re-created a conda environment and installed foldseek with
conda install -c conda-forge -c bioconda foldseek
Still getting the error, as follows:
easy-search AF-A0A0G2KTI4-F1-model_v2_AFCT-OUT_single_A130-1136.pdb /data/cltam/script/foldseek/database/ foldseek_aln.m8 tmpFolder
MMseqs Version: 3.915ef7d
Seq. id. threshold 0
Coverage threshold 0
Coverage mode 0
Max reject 2147483647
Max accept 2147483647
Add backtrace false
TMscore threshold 0.5
TMalign fast 1
Preload mode 0
Threads 128
Verbosity 3
Substitution matrix aa:3di.out,nucl:3di.out
Alignment mode 3
Alignment mode 0
E-value threshold 0.001
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Max sequence length 65535
Compositional bias 1
Compositional bias 1
Gap open cost aa:10,nucl:10
Gap extension cost aa:1,nucl:1
Compressed 0
Seed substitution matrix aa:3di.out,nucl:3di.out
Sensitivity 9.5
k-mer length 6
k-score seq:2147483647,prof:2147483647
Max results per query 1000
Split database 0
Split mode 2
Split memory limit 0
Diagonal scoring true
Exact k-mer matching 0
Mask residues 0
Mask residues probability 0.99995
Mask lower case residues 0
Minimum diagonal score 15
Spaced k-mers 1
Spaced k-mer pattern
Local temporary path
Alignment type 2
Remove temporary files true
MPI runner
Force restart with latest tmp false
Chain name mode 0
Write lookup file 1
Tar Inclusion Regex .*
Tar Exclusion Regex ^$
Alignment format 0
Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits
Database output false
createdb /data/cltam/script/foldseek/database/ tmpFolder/1910639421338238365/target --chain-name-mode 0 --write-lookup 1 --tar-include '.*' --tar-exclude '^$' --threads 128 -v 3
Output file: tmpFolder/1910639421338238365/target
Error: target createdb died
There is a file name missing in this path:
/data/cltam/script/foldseek/database/
That looks like a directory. You need to point it to a database.