Foldseek Segmentation fault => Error: target createdb died

[kchennen]

Expected Behavior

Searching Alphafold/UniProt database with a domain PDB file (406 AA). Ex online: https://search.foldseek.com/result/gDrI9s90OiVzH1Bl_4llQxgS3c02yXxavhnhjg/0

Current Behavior

Crash with a segmentation fault error each time (even when changing the input file) at the same step of "Error: target createdb died"

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

Foldssek Output (for bugs)

Please make sure to also post the complete output of Spacepharer. You can use gist.github.com for large output.

❯ foldseek easy-search ../raw_cegal_mhd_pdb/P04386_GAL4_MHD.pdb /commun/db/foldseek P04386_GAL4_MHD tmp
easy-search ../raw_cegal_mhd_pdb/P04386_GAL4_MHD.pdb /commun/db/foldseek P04386_GAL4_MHD tmp

MMseqs Version: ef4e960
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 64
Verbosity 3
LDDT threshold 0
Sort by structure bit score 1
Alignment type 2
Substitution matrix aa:3di.out,nucl:3di.out
Alignment mode 3
Alignment mode 0
E-value threshold 10
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
Target search mode 0
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 30
Selected taxa
Spaced k-mers 1
Spaced k-mer pattern
Local temporary path
Exhaustive search mode false
Prefilter mode 0
Search iterations 1
Remove temporary files true
MPI runner
Force restart with latest tmp false
Cluster search 0
Chain name mode 0
Write mapping file 0
Mask b-factor threshold 0
Coord store mode 2
Write lookup file 1
Tar Inclusion Regex .*
Tar Exclusion Regex ^$
File Inclusion Regex .*
File Exclusion Regex ^$
Alignment format 0
Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits
Database output false
Greedy best hits false

createdb /commun/db/foldseek tmp/3337267339239327975/target --chain-name-mode 0 --write-mapping 0 --mask-bfactor-threshold 0 --coord-store-mode 2 --write-lookup 1 --tar-include '.' --tar-exclude '^$' --file-include '.' --file-exclude '^$' --threads 64 -v 3

Output file: tmp/3337267339239327975/target
Segmentation fault (core dumped) ] 37.00% 79.43M eta 2m 17s
Error: target createdb died

Context

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

• 1. I am trying to search proteins having the same fold as a domain of interest in Alphafold/UniProt database
• 2. Trying to filter and sort the results by score and length of hit (currently not possible online)
• 3. Have the batch results (currently cannot download the results with the online website)

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 foldseek without any parameters):

foldseek Version: ef4e960

• Which foldseek version was used (Statically-compiled, self-compiled, Conda, etc.): Conda
• 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):

processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 85
model name : Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
stepping : 4
microcode : 0x2006e05
cpu MHz : 3544.754
cache size : 22528 KB
physical id : 0
siblings : 32
core id : 0
cpu cores : 16
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 22
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke md_clear flush_l1d arch_capabilities

• Operating system and version:

Distributor ID: Ubuntu
Description: Ubuntu 18.04.3 LTS
Release: 18.04
Codename: bionic

[milot-mirdita]

The error looks like you didn't pass the correct path to the AFDB as target database. Please check if the /commun/db/foldseek path was intended.