hhsearch segmentation fault

[ajrferrari]

I am running hhsearch (HHsearch 3.3.0) with the following parameters

CPU="10" MEM="12" DB="$PIPEDIR/pdb100_2020Mar11/pdb100_2020Mar11"

HH="$softwares/hh-suite/build/bin/hhsearch -b 50 -B 500 -z 50 -Z 500 -mact 0.05 -cpu $CPU -maxmem $MEM -aliw 100000 -e 100 -p 5.0 -d $DB"

$HH -i $WDIR/t000.msa0.ss2.a3m -o $WDIR/t000.hhr

This is the log file which states there is a segmentation fault happening

• 13:30:43.343 INFO: /home/allan/POSTDOC/Predictions/GH1/trRosetta2/benchmark/1BGGA/t000_.msa0.ss2.a3m is in A2M, A3M or FASTA format

• 13:30:43.552 INFO: Searching 136710 database HHMs without prefiltering

• 13:30:43.628 INFO: Iteration 1

• 13:30:43.748 INFO: Scoring 136710 HMMs using HMM-HMM Viterbi alignment

• 13:30:44.004 INFO: Alternative alignment: 0

• 13:31:13.420 INFO: 136710 alignments done

• 13:31:13.843 INFO: Alternative alignment: 1

• 13:31:16.036 INFO: 6118 alignments done

• 13:31:16.043 INFO: Alternative alignment: 2

• 13:31:16.343 INFO: 681 alignments done

• 13:31:16.343 INFO: Alternative alignment: 3

• 13:31:16.387 INFO: 64 alignments done

Segmentation fault (core dumped)

See attached the t000.msa0.ss2.a3m.gz [t000.msa0.ss2.a3m.gz](https://github.com/soedinglab/hh-suite/files/6760244/t000_.msa0.ss2.a3m.gz) file.

I'm running the source github code I just have installed. The same error was happening from the conda version. Any help on this?

[milot-mirdita]

Please run the hhsearch in gdb:

gdb --args $HH -i $WDIR/t000_.msa0.ss2.a3m -o $WDIR/t000_.hhr

Then press r (run) and enter and then once it crashes bt (backtrace) and enter. Copy paste the output here please.

[ajrferrari]

Hi Milot,

Here is the output (same for conda and built from source versions)

0 0x00005555555e3d6c in HHDatabaseEntry::getTemplateA3M(Parameters&,

float, float const () [20], float const (*) [20], Alignment&) ()

1 0x0000555555575372 in HHblits::mergeHitsToQuery(HitList&, Hash*,

Hash*, int&, int&, int) ()

2 0x000055555557e482 in HHblits::premerge(Hash, Hash, int&,

int&, int) ()

3 0x0000555555580dba in HHblits::run(_IO_FILE, char) ()

4 0x00005555555703dd in main ()

On Sun, Jul 4, 2021 at 5:44 PM Milot Mirdita @.***> wrote:

Please run the hhsearch in gdb:

gdb --args $HH -i $WDIR/t000.msa0.ss2.a3m -o $WDIR/t000.hhr

Then press r (run) and enter and then once it crashes bt (backtrace) and enter. Copy paste the output here please.

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[jiaxiang-wu]

Hi @ajrferrari

Are you using the RoseTTAFold repo from RosettaCommons? I have encountered the same segmentation fault issue when running hhsearch. Downgrading hh-suite from v3.3.0 to v3.2.0 works for me (compiling from source). Maybe you can also give it a try.

Best,

[martin-steinegger]

@jiaxiang-wu @ajrferrari we added the pre-merge back to HHblits. It looks like this is causing the issues. You can avoid using the premerge by setting -premerge to 0.

[jiaxiang-wu]

@martin-steinegger Got it! Thanks for your reply!

[martin-steinegger]

I have looked at the issues. It seems that the PDB100 database does not contain an _a3m database. HHblits requires it to load sequences for the premerge. I would contact the Baker group and ask to add the a3m files.

[ajrferrari]

@jiaxiang-wu @martin-steinegger I tried to run it with the -premerge 0 flag but it returned the same error.

gdb --args $HH -i $WDIR/t000.msa0.ss2.a3m -o $WDIR/t000.hhr -premerge 0

0x000000000047f304 in HHDatabaseEntry::getTemplateA3M(Parameters&, float, float const () [20], float const (*) [20], Alignment&) () (gdb) bt

0 0x000000000047f304 in HHDatabaseEntry::getTemplateA3M(Parameters&,

float, float const () [20], float const (*) [20], Alignment&) ()

1 0x000000000041e63a in HHblits::mergeHitsToQuery(HitList&, Hash*,

Hash*, int&, int&, int) ()

2 0x000000000042487f in HHblits::premerge(Hash, Hash, int&,

int&, int) ()

3 0x00000000004273ee in HHblits::run(_IO_FILE, char) ()

4 0x0000000000419b2d in main ()

Meanwhile, I also ask them for the _a3m database to be included in the PDB100.

On Mon, Jul 5, 2021 at 1:58 AM Martin Steinegger @.***> wrote:

I have looked at the issues. It seems that the PDB100 database does not contain an _a3m database. HHblits requires it to load sequences for the premerge. I would contact the Baker group and ask to add the a3m files.

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-- Állan

[milot-mirdita]

Please pull the latest commit again and recompile. -premerge was only parsed in hhblits.

[milot-mirdita]

We will make a new release soon, there were quite a few important bug fixes since the last release.

[ajrferrari]

Thank you, @milot-mirdita, it worked! Waiting for the new release!

[moonblue333]

This is OK for me. (context: RosettaCommons/RoseTTAFold) wget https://github.com/soedinglab/hh-suite/releases/download/v3.2.0/hhsuite-3.2.0-AVX2-Linux.tar.gz --no-check-certificate tar xvfz hhsuite-3.2.0-AVX2-Linux.tar.gz

[ksteczk]

We will make a new release soon, there were quite a few important bug fixes since the last release.

Just for making longer plans, I'd like to ask whether a new release is planned or all bug fixes were already included and we're good to go with the current version? Do you plan any substantial changes in the functioning of the programs (eg. ffindex stuff) or everything will stay as it is?