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Better Alignments with Translated HMMER
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install issue and core dump #1

Closed dcopetti closed 1 year ago

dcopetti commented 1 year ago

Hello,

I installed FraHMMER on our cluster and at the last step I got a permission error:

$ make install
     SUBDIR easel
     SUBDIR miniapps
     SUBDIR libdivsufsort
     SUBDIR src
     SUBDIR impl_sse
     SUBDIR profmark
if [ ! -d /usr/local/bin ]; then /usr/bin/install -c -d /usr/local/bin; fi
if [ ! -d /usr/local/share/man/man1 ]; then /usr/bin/install -c -d /usr/local/share/man/man1; fi
make -C src install
make[1]: Entering directory '/newwing/wing2/users/dcopetti/bin/FraHMMER/src'
for file in frahmmer frahmmbuild frahmmconvert frahmmfetch frahmmstat; do \
   /usr/bin/install -c -m 0755 $file /usr/local/bin/ ;\
done
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmer': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmbuild': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmconvert': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmfetch': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmstat': Permission denied
make[1]: *** [Makefile:321: install] Error 1
make[1]: Leaving directory '/newwing/wing2/users/dcopetti/bin/FraHMMER/src'
make: *** [Makefile:135: install] Error 2

I am working with my sys admin to resolve it.

I am still able to run frahmmer, with -h I see the parameters. I can't find the executable for frahmmsearchthough: is it because of the error at the make install command above?

I tried running frahmmer as frahmmer --cpu 48 -o output --tblout output.tab query.fa genome.fa with the query being a unaligned multifasta of 5 protein sequences. Can I do the alignment with frahmmeror fo I need frahmmsearch? If so, where do I find it? Thanks!

traviswheeler commented 1 year ago

That's a permissions issue. You can either (1) run 'make install' with root privileges, or (2) run the 'configure' commands with the extra flag '-- prefix=$HOME' ... This will place the binaries in ~/bin

dcopetti commented 1 year ago

Thanks, the installation issue is solved! There is a /bin folder now, with the following executables in there:

total 2.5M
-rwxr-xr-x 1 dcopetti bioinfo 1.3M Oct 13 14:10 frahmmer
-rwxr-xr-x 1 dcopetti bioinfo 1.1M Oct 13 14:10 frahmmbuild
-rwxr-xr-x 1 dcopetti bioinfo 1.1M Oct 13 14:10 frahmmconvert
-rwxr-xr-x 1 dcopetti bioinfo 837K Oct 13 14:10 frahmmfetch
-rwxr-xr-x 1 dcopetti bioinfo 832K Oct 13 14:10 frahmmstat

I still can't find the frahmmsearchexecutable though, and if I run frahmmerI get a core dump error:

frahmmer --cpu 48 -o output --tblout output.tab query.fa genome.fa
Segmentation fault (core dumped)

with empty output files only. what is missing? thanks

traviswheeler commented 1 year ago

First: thanks for the note about the frahmmsearch problem - we'll get the documentation updated.

As for the core dump: (1) What OS are you running? *e.g. send the results of 'cat /etc/os-release' (2) Can you provide an example of versions of the query.fa and genome.fa files that cause the error to reproduce?

AGI-chandler commented 1 year ago

Hi, sys admin here. Here's some info you requested:

$ cat /etc/os-release
NAME="CentOS Linux"
VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-8"
CENTOS_MANTISBT_PROJECT_VERSION="8"

$ cat query.fa
>S1__Schlumbergera_truncata
MTMILVTFILLNLLSPFYCYDYMQFVQTWPLTHCTVVVRRCSTPIIRDNFTIHGVWEEFNRFTGRRNCNTPTSSAFNRSLVAHLEHQLNASWPYLANRNNNVYIWTHEWNSHGKCLEPTFNVVSYFQLGLRWKSRYNILEILTRHGFAPGAVYDVTLMKDAIKNETGGIDPIMSCKPSPNRPHYLYEVRLCLDSRGQQLISCASKGLADKCPTNTTTVFFP
>S2__Schlumbergera_truncata
MTRTYILITLLALAFFLSSYDCYDYMLFAQIWPPGYCSVNRCSMPIPNDFTIHGIWDQYNSGKRGPGNCTGTPFNLTLVAQFETALNASWPNLKNQRNNQKFWKHEWEAHGTCLEPTVTVPSYFKLALGWKNRLNILGFLTTQGYAPGRGVNYPSSSIRNAVIATVKVEPVLHCLGNGSHTFLLEVRLCMDYQGQKLISCAGKKLNDTCKSNSIYFPQ
>S3__Schlumbergera_truncata
MRTVTNIITTVSLLAFLLPSFHSHDYMKFVQTWPPTYCTVNNCSRPIINDRFTIHGIWQAYNSRGAAPPCMATNFSFRAVAHLERQLNWHWPSLKNPRNNRRFWEHEWSIHGICLQPVFNVTTYFRRGLDLMNQYNLLDILTSSGHDPDPQVTYNLASMQTAIQTAIGGVTPLLKCVQKSNSTNYLLYEVVVCLGYHGQPLIPCLGTGSCPPQNISWSL
>S4__Schlumbergera_truncata
MTRSIFAVIPLTLLLPAFYCVHDYLIFVQTWPPSFCRIDRCFGPGINNQFTIHGVWDGYYNRRHANGPCTSTNFSRALVAHIERQLNASWPNLKDQNNNDIIWTHEWKKHGTCLEPFVDVTTYFELGLALMRRYPLYDFLRSHGYPPGPGKTYDTNLMRNAIRSMTGSFPVLFCKHGTNRTGNPLLLEVRFCFDSQGLHPINCTAGSCPSQFVSFP
>S5__Schlumbergera_truncata
MAKITAIFFAFLLISSHCVHDYLIHVETWPPSYCRINRCSGPNINNRFTIHGVWDAYYNGQYGVGPCTSNNFSRTMVANIERRLNISWPNLKDQSNNEELWIHEWDRHGTCLEPFVNVTTYFELGLDLKHRYPILNFLRGNGINHGQRYLTSRMRNAIQLGIGGSAPVLICKNVPNQTDPFLIEVRLCFDSRGSQPIRCTARSCGSRYIMFP

genome.fa is 1.1G so let us know what info you want about it. Here is some core dump info if that helps. Would it help to recompile with debugging enabled?

# coredumpctl debug 82945
           PID: 82945 (frahmmer)
        Signal: 11 (SEGV)
  Command Line: frahmmer --cpu 48 -o output --tblout output.tab --qformat fasta query.fa genome.fa
[...]
       Message: Process 82945 (frahmmer) of user 10022 dumped core.

                Stack trace of thread 82972:
                #0  0x0000000000490888 esl_gencode_GetTranslation (frahmmer)
                #1  0x000000000049161b esl_gencode_ProcessPiece (frahmmer)
                #2  0x000000000040b873 p7_bg_fs_FilterScore (frahmmer)
                #3  0x000000000041facc p7_Pipeline_Frameshift (frahmmer)
                #4  0x0000000000406951 pipeline_thread (frahmmer)
                #5  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #6  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82953:
                #0  0x0000000000406f47 p7_FLogsum (frahmmer)
                #1  0x000000000044f293 p7_ForwardParser_Frameshift (frahmmer)
                #2  0x000000000041fb17 p7_Pipeline_Frameshift (frahmmer)
                #3  0x0000000000406951 pipeline_thread (frahmmer)
                #4  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #5  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82988:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82955:
                #0  0x00007ffff75607db __mprotect (libc.so.6)
                #1  0x00007ffff74eca72 sysmalloc (libc.so.6)
                #2  0x00007ffff74edaa9 _int_malloc (libc.so.6)
                #3  0x00007ffff74eec72 malloc (libc.so.6)
                #4  0x00000000004c7415 sq_createblock (frahmmer)
                #5  0x00000000004c8205 esl_sq_CreateDigitalBlock (frahmmer)
                #6  0x000000000041f1d5 p7_Pipeline_Frameshift (frahmmer)
                #7  0x0000000000406a13 pipeline_thread (frahmmer)
                #8  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #9  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82945:
                #0  0x00007ffff75565d4 __read (libc.so.6)
                #1  0x00007ffff74e545b _IO_file_xsgetn (libc.so.6)
                #2  0x00007ffff74da5eb _IO_fread (libc.so.6)
                #3  0x00000000004cd4b6 loadmem.part.0 (frahmmer)
                #4  0x00000000004cd773 loadbuf (frahmmer)
                #5  0x00000000004cea18 read_nres (frahmmer)
                #6  0x00000000004cf23c sqascii_ReadWindow (frahmmer)
                #7  0x00000000004d04e3 sqascii_ReadBlock (frahmmer)
                #8  0x0000000000403c73 main (frahmmer)
                #9  0x00007ffff748c493 __libc_start_main (libc.so.6)
                #10 0x000000000040583e _start (frahmmer)

                Stack trace of thread 82954:
                #0  0x000000000044f2c9 p7_ForwardParser_Frameshift (frahmmer)
                #1  0x000000000041fb17 p7_Pipeline_Frameshift (frahmmer)
                #2  0x0000000000406a13 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82957:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82956:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82958:
                #0  0x0000000000453465 p7_GViterbi (frahmmer)
                #1  0x000000000041a100 p7_pli_ExtendAndMergeORFs.part.0 (frahmmer)
                #2  0x000000000042046e p7_Pipeline_Frameshift (frahmmer)
                #3  0x0000000000406a13 pipeline_thread (frahmmer)
                #4  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #5  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82959:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82950:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82994:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82951:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82961:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82963:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82960:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82965:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82962:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82966:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82952:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82996:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82975:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82993:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82964:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82976:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82981:
                #0  0x0000000000406f28 p7_FLogsum (frahmmer)
                #1  0x000000000044f258 p7_ForwardParser_Frameshift (frahmmer)
                #2  0x000000000041fb17 p7_Pipeline_Frameshift (frahmmer)
                #3  0x0000000000406a13 pipeline_thread (frahmmer)
                #4  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #5  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82949:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82978:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82971:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82980:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82969:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82970:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82983:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82973:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82985:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82982:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82979:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82974:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82984:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82986:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82989:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82990:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82987:
                #0  0x00007ffff75607db __mprotect (libc.so.6)
                #1  0x00007ffff74eca72 sysmalloc (libc.so.6)
                #2  0x00007ffff74edaa9 _int_malloc (libc.so.6)
                #3  0x00007ffff74eec72 malloc (libc.so.6)
                #4  0x00000000004c7415 sq_createblock (frahmmer)
                #5  0x00000000004c8205 esl_sq_CreateDigitalBlock (frahmmer)
                #6  0x000000000041f1d5 p7_Pipeline_Frameshift (frahmmer)
                #7  0x0000000000406a13 pipeline_thread (frahmmer)
                #8  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #9  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82968:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82967:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82991:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82992:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82977:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

                Stack trace of thread 82995:
                #0  0x00007ffff7bbe3fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)
                #1  0x00000000004eb49b esl_workqueue_WorkerUpdate (frahmmer)
                #2  0x0000000000406820 pipeline_thread (frahmmer)
                #3  0x00007ffff7bb817a start_thread (libpthread.so.0)
                #4  0x00007ffff7565dc3 __clone (libc.so.6)

GNU gdb (GDB) Red Hat Enterprise Linux 8.2-15.el8
[...]
Reading symbols from frahmmer...(no debugging symbols found)...done.
[New LWP 82972]
[New LWP 82953]
[New LWP 82988]
[New LWP 82955]
[New LWP 82945]
[New LWP 82954]
[New LWP 82957]
[New LWP 82956]
[New LWP 82958]
[New LWP 82959]
[New LWP 82950]
[New LWP 82994]
[New LWP 82951]
[New LWP 82961]
[New LWP 82963]
[New LWP 82960]
[New LWP 82965]
[New LWP 82962]
[New LWP 82966]
[New LWP 82952]
[New LWP 82996]
[New LWP 82975]
[New LWP 82993]
[New LWP 82964]
[New LWP 82976]
[New LWP 82981]
[New LWP 82949]
[New LWP 82978]
[New LWP 82971]
[New LWP 82980]
[New LWP 82969]
[New LWP 82970]
[New LWP 82983]
[New LWP 82973]
[New LWP 82985]
[New LWP 82982]
[New LWP 82979]
[New LWP 82974]
[New LWP 82984]
[New LWP 82986]
[New LWP 82989]
[New LWP 82990]
[New LWP 82987]
[New LWP 82968]
[New LWP 82967]
[New LWP 82991]
[New LWP 82992]
[New LWP 82977]
[New LWP 82995]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `frahmmer --cpu 48 -o output --tblout output.tab --qformat fasta query.fa genome.fa'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x0000000000490888 in esl_gencode_GetTranslation ()
[Current thread is 1 (Thread 0x7fffe77b1700 (LWP 82972))]
(gdb)

Not too familiar with gdb so not sure what to do next.

dcopetti commented 1 year ago

THank you @AGI-chandler ! @traviswheeler : I will share the reference privately

GenevieveKrause commented 1 year ago

If you do a git pull it should resolve the issue. Let me know if you have any other problems.

dcopetti commented 1 year ago

It works now! I did the git pull, re-run the configure and make steps and it runs Thanks!