Errors related to makeblastdb

[alopgar]

I am trying to use RepeatMasker in a remote linux server, but I am receiving several errors both during the configuration and the execution of the program.

Installation: I installed and configured RepeatMasker as follows:

$ wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz
$ tar -zxvf RepeatMasker-4.1.5.tar.gz
$ cd RepeatMasker
$ perl ./configure
-- Setting perl interpreter...
Can't open DateRepeats: No such file or directory.

RepeatMasker Configuration Program

Checking for libraries...

  - Found Dfam

/usr/bin/which: no trf in (/home/adrianl/perl5/bin:(...):/home/adrianl/bin)

The full path including the name for the TRF program.
TRF_PRGM: /home/adrianl/Programs/TRF-4.09.1/build/src/trf

Add a Search Engine:
2. RMBlast: 
/usr/bin/which: no RMBLAST in (/home/adrianl/perl5/bin:(...):/home/adrianl/bin)
RMBLAST_DIR: /home/adrianl/Programs/rmblast-2.14.0/bin

Add a Search Engine:
   2. RMBlast: [ Configured, Default ]
   5. Done

Enter Selection: 5
Building FASTA version of RepeatMasker.lib ....................................................
Building RMBlast frozen libraries..
sh: line 1:  3477 Bus error               /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb -dbtype nucl -in /home/adrianl/Programs/RepeatMasker/Libraries/RepeatMasker.lib > /dev/null 2>&1
sh: line 1:  3488 Bus error               /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb -dbtype prot -in /home/adrianl/Programs/RepeatMasker/Libraries/RepeatPeps.lib > /dev/null 2>&1
The program is installed with a the following repeat libraries:
File: /home/adrianl/Programs/RepeatMasker/Libraries/Dfam.h5
FamDB Generator: famdb.py v0.4.2
FamDB Format Version: 0.5
FamDB Creation Date: 2023-01-08 10:42:05.645898

Database: Dfam
Version: 3.7
Date: 2023-01-11

Dfam - A database of transposable element (TE) sequence alignments and HMMs.

Total consensus sequences: 19768
Total HMMs: 19730

Further documentation on the program may be found here:
  /home/adrianl/Programs/RepeatMasker/repeatmasker.help

After, I try to use it with the output of a RepeatModeler command. The pipeline I followed is this one:

printf "Building repeat database...\n"
~/Programs/RepeatModeler-2.0.4/BuildDatabase -name Sample1_repdb ~/Results/seqs/Sample1.final.contigs.euk.1k.fa
printf "Running RepeatModeler...\n"
~/Programs/RepeatModeler-2.0.4/RepeatModeler -database Sample1_repdb -threads 20 -LTRStruct
printf "Running RepeatMasker...\n"
~/Programs/RepeatMasker/RepeatMasker -lib Sample1_repdb-families.fa -xsmall ~/Results/seqs/Sample1.final.contigs.euk.1k.fa -pa 20

And this is the output I get from RepeatMasker:

Running RepeatMasker...
RepeatMasker version 4.1.5
Search Engine: NCBI/RMBLAST [ 2.14.0+ ]
sh: line 1: 115784 Bus error               /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb -out /home/adrianl/Results/genemark/Sample1/RM_115730.TueJul41013342023/Sample1_repdb-families.fa -dbtype nucl -in Sample1_repdb-families.fa > /home/adrianl/Results/genemark/Sample1/RM_115730.TueJul41013342023/makeblastdb.log 2>&1
Using Custom Repeat Library: Sample1_repdb-families.fa

  It appears that RepeatMasker attempted to generate a cached general library
  before but didn't complete it.  Attempting to remove and rebuild this
  cache: /home/adrianl/Programs/RepeatMasker/Libraries//general.working

Building general libraries in: /home/adrianl/Programs/RepeatMasker/Libraries//general
sh: line 1: 115896 Bus error               /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb -dbtype nucl -in /home/adrianl/Programs/RepeatMasker/Libraries//general.working/is.lib > /home/adrianl/Programs/RepeatMasker/Libraries//general.working//rmblastdb.log 2>&1
RepeatMasker::createLib(): Error invoking /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb on file /home/adrianl/Programs/RepeatMasker/Libraries//general.working/is.lib.

I tried to re-run the configure script but the result is the same. How can I solve this?

My OS:

NAME="CentOS Linux"
VERSION="7 (Core)"

[rmhubley]

The problem appears to be with the RMBlast package. How did you obtain and install it? As a quick test could you run:

'ldd /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb'

and provide the output?

[rmhubley]

If this is still a problem please let us know.

[alopgar]

Sorry for the delay, I have been not able to continue evaluating this since now. This seems to be still a problem, I tried to re-configure the search engine and the bus error appeared again. The RMBlast package was installed as follows:

wget https://www.repeatmasker.org/rmblast/rmblast-2.14.0+-x64-linux.tar.gz
tar -zxvf rmblast-2.14.0+-x64-linux.tar.gz

As you asked, I tried the command provided. Here is the output:

$ ldd /home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb
    linux-vdso.so.1 =>  (0x00007ffdd1fa4000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff1d9b18000)
    libz.so.1 => /lib64/libz.so.1 (0x00007ff1d9902000)
    libbz2.so.1 => /lib64/libbz2.so.1 (0x00007ff1d96f2000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00007ff1d94ee000)
    libresolv.so.2 => /lib64/libresolv.so.2 (0x00007ff1d92d5000)
    libm.so.6 => /lib64/libm.so.6 (0x00007ff1d8fd3000)
    libgomp.so.1 => /lib64/libgomp.so.1 (0x00007ff1d8dad000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff1d8b97000)
    libc.so.6 => /lib64/libc.so.6 (0x00007ff1d87ca000)
    /lib64/ld-linux-x86-64.so.2 (0x00007ff1d9d34000)

[rmhubley]

Do you get the buss error if you run this by hand:

/home/adrianl/Programs/rmblast-2.14.0/bin/makeblastdb -dbtype nucl -in /home/adrianl/Programs/RepeatMasker/Libraries/RepeatMasker.lib

Is it repeatable?

[alopgar]

Yes, doing it by hand outputs also a bus error.

What do you mean by repeatable?