Open kcibul-aeratx opened 2 years ago
I ran the final command (result2profile) in gdb with
gdb --args /mnt/disks/kc-ssd/MMseqs2/build/bin/mmseqs result2profile profiles/CLUSTER_100005_profile /mnt/disks/kc-ssd/GURARB/GURARB_cluster75_reps.idx /tmp/15358673946673749737/aln_0 /tmp/15358673946673749737/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.001 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 2 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --gap-pc 10 --threads 32 --compressed 0 -v 3
and got the following backtrace via bt
(gdb) #0 0x0000555555a8d42b in tantan::Tantan::calcForwardTransitionAndEmissionProbs() ()
#1 0x0000555555a8d865 in tantan::Tantan::calcRepeatProbs(float*) ()
#2 0x0000555555a8bf8b in tantan::getProbabilities(char const*, char const*, int, double const* const*, double, double, double, double, double, float*) ()
#3 0x0000555555a8be7f in tantan::maskSequences(char*, char*, int, double const* const*, double, double, double, double, double, double, char const*) ()
#4 0x000055555597de9b in PSSMMasker::mask(Sequence&, float, PSSMCalculator::Profile&) ()
#5 0x00005555559f918b in result2profile(int, char const**, Command const&, bool) [clone ._omp_fn.0] ()
#6 0x00007ffff7c7c4c2 in GOMP_parallel () from /lib/x86_64-linux-gnu/libgomp.so.1
#7 0x00005555559f86d7 in result2profile(int, char const**, Command const&, bool) ()
#8 0x00005555559f887c in result2profile(int, char const**, Command const&) ()
#9 0x00005555557ea0d5 in runCommand(Command*, int, char const**) ()
#10 0x00005555557eb00a in main ()
Recompiled in Debug mode, more details
Thread 1 "mmseqs" received signal SIGSEGV, Segmentation fault.
0x0000555555a8d40b in tantan::Tantan::calcForwardTransitionAndEmissionProbs (this=0x7ffffffbaaa0)
at /mnt/disks/kc-ssd/MMseqs2/src/commons/tantan.cpp:319
319 foregroundBeg[i] = (b * b2fProbs[i] + f * f2f0) * lrRow[(int)seqPtr[-i-1]];
(gdb) bt
#0 0x0000555555a8d40b in tantan::Tantan::calcForwardTransitionAndEmissionProbs (this=0x7ffffffbaaa0)
at /mnt/disks/kc-ssd/MMseqs2/src/commons/tantan.cpp:319
#1 0x0000555555a8d845 in tantan::Tantan::calcRepeatProbs (this=0x7ffffffbaaa0, letterProbs=0x555556582704)
at /mnt/disks/kc-ssd/MMseqs2/src/commons/tantan.cpp:373
#2 0x0000555555a8bf6b in tantan::getProbabilities (
seqBeg=0x5555564e06c0 "\025\025\025\025\025\025\025\n\f\003\v\020\f\016\020\020\016\017", seqEnd=0x5555564e07b9 "",
maxRepeatOffset=50, likelihoodRatioMatrix=0x55555643d8f0, repeatProb=0.0050000000000000001, repeatEndProb=0.050000000000000003,
repeatOffsetProbDecay=0.90000000000000002, firstGapProb=0, otherGapProb=0, probabilities=0x555556582700)
at /mnt/disks/kc-ssd/MMseqs2/src/commons/tantan.cpp:470
#3 0x0000555555a8be5f in tantan::maskSequences (
seqBeg=0x5555564e06c0 "\025\025\025\025\025\025\025\n\f\003\v\020\f\016\020\020\016\017", seqEnd=0x5555564e07b9 "",
maxRepeatOffset=50, likelihoodRatioMatrix=0x55555643d8f0, repeatProb=0.0050000000000000001, repeatEndProb=0.050000000000000003,
repeatOffsetProbDecay=0.90000000000000002, firstGapProb=0, otherGapProb=0, minMaskProb=0.89999997615814209,
maskTable=0x7ffffffdc530 '\024' <repeats 200 times>...) at /mnt/disks/kc-ssd/MMseqs2/src/commons/tantan.cpp:449
#4 0x000055555597de7b in PSSMMasker::mask (this=0x7ffffffbaca0, centerSequence=..., maskProb=0.899999976, pssmRes=...)
at /mnt/disks/kc-ssd/MMseqs2/src/alignment/PSSMMasker.h:25
#5 0x00005555559f916b in result2profile () at /mnt/disks/kc-ssd/MMseqs2/src/util/result2profile.cpp:262
#6 0x00007ffff7c7c4c2 in GOMP_parallel () from /lib/x86_64-linux-gnu/libgomp.so.1
#7 0x00005555559f86b7 in result2profile (argc=54, argv=0x7fffffffe138, command=..., returnAlnRes=false)
at /mnt/disks/kc-ssd/MMseqs2/src/util/result2profile.cpp:140
#8 0x00005555559f885c in result2profile (argc=54, argv=0x7fffffffe138, command=...)
at /mnt/disks/kc-ssd/MMseqs2/src/util/result2profile.cpp:311
#9 0x00005555557ea0b5 in runCommand (p=0x55555641eac0, argc=54, argv=0x7fffffffe138)
at /mnt/disks/kc-ssd/MMseqs2/src/commons/Application.cpp:40
#10 0x00005555557eafea in main (argc=56, argv=0x7fffffffe128) at /mnt/disks/kc-ssd/MMseqs2/src/commons/Application.cpp:203
Can you try to remove the precomputed index? It seems to have been generated by a different version than the one you use to run.
You can also set the MMSEQS_IGNORE_INDEX environment variable to ignore the precomputed index during the run.
Would it be possible to upload the query/target set that is crashing?
Expected Behavior
Not crashing, with a better error message if this is a user problem
Current Behavior
Seg Fault. 90% of profile searches are fine against this database, but others segfault. example below
Steps to Reproduce (for bugs)
MMseqs Output (for bugs)
Context
Your Environment
Include as many relevant details about the environment you experienced the bug in.