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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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all to all alignment failed with error 13. #122

Open TomDongmin opened 1 year ago

TomDongmin commented 1 year ago

I am trying to align 831 alphafold-predicted PDBs and the program stops running with the following error:

Failed to execute tmp/10218790963214741954/easystructuresearch.sh with error 13.

The job was run on high performance computing cluster using conda-installed foldseek. Thank you in advance!

Create directory tmp1 easy-search /rds/general/user/tdkim/projects/molecular_evolution_lab/live/D1_str_TDK/D1_r1_DP /rds/general/user/tdkim/projects/molecular_evolution_lab/live/D1_str_TDK/D1_r1_DP aln tmp1 --alignment-type 1 --tmscore-threshold 0.0 --format-output query,target,alntmscore,u,t --exhaustive-search 1 -e inf

MMseqs Version: 5.53465f0 Seq. id. threshold 0 Coverage threshold 0 Coverage mode 0 Max reject 2147483647 Max accept 2147483647 Add backtrace false TMscore threshold 0 TMalign hit order 0 TMalign fast 1 Preload mode 0 Threads 256 Verbosity 3 LDDT threshold 0 Sort by structure bit score 1 Substitution matrix aa:3di.out,nucl:3di.out Alignment mode 3 Alignment mode 0 E-value threshold inf 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 1 Minimum diagonal score 15 Selected taxa
Spaced k-mers 1 Spaced k-mer pattern
Local temporary path
Exhaustive search mode true Search iterations 1 Alignment type 1 Remove temporary files true MPI runner
Force restart with latest tmp false Chain name mode 0 Mask b-factor threshold 0 Coord store mode 2 Write lookup file 1 Tar Inclusion Regex .* Tar Exclusion Regex ^$ Alignment format 0 Format alignment output query,target,alntmscore,u,t Database output false

Alignment backtraces will be computed, since they were requested by output format.

martin-steinegger commented 1 year ago

From the current issue, it is hard to know what might cause the issue. Could you please provide a minimal example for use to investigate it?

TomDongmin commented 1 year ago

Thank you for your prompt reply! Here is a sample set from the dataset. Thank you again for your help.

martin-steinegger commented 1 year ago

Unfortunately I can not see it in github.

TomDongmin commented 1 year ago

My apologies, I attached to the email, not here. Here is the file, thank you![ D1_samG.zip

TomDongmin commented 1 year ago

Hi, I wonder how it is going with the investigation, I tried the web server with one of the sequences and it works great! But I am also interested in all to all for global variability analysis in relation to the protein's evolutionary history. I think your method is very powerful and can provide great insights on my project. I am looking forward to hearing from you. Thank you in advance!

martin-steinegger commented 9 months ago

@TomDongmin does the issue still persists in the newest version?