Question: error RepeatMasker Installation
0
gravatar for frida
4 weeks ago by
frida10
rome
frida10 wrote:

I was installing repeatsmasker and it apparently seems to work because it shows "Congratulations! RepeatMasker is now ready to use." But when I run it it reports "Can't locate Text/Soundex.pm...". so I installed the module by "sudo cpan Text::Soundex", and by the end it tells me "Text::Soundex is up to date (3.05)." It seems the module is already installed, but RepeatMasker still has the same problem, as I'll show you in this code:

fragua@picci:~/RM/RepeatMasker$ sudo cpan Text::Soundex
Loading internal null logger. Install Log::Log4perl for logging messages
Reading '/home/fragua/.cpan/Metadata'
  Database was generated on Fri, 19 Apr 2019 22:17:03 GMT
Text::Soundex is up to date (3.05).

fragua@picci:~/RM/RepeatMasker$ ./RepeatMasker -s -lib /home/fragua/RepeatScout-1.0.5/ObiINK5k_repeats_filtered1.fasta /home/fragua/Documenti/Workdirectory/ObiINC5k.fa
Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /home/fragua/RM/RepeatMasker /home/fragua/perl5/lib/perl5 /home/fragua/anaconda/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/fragua/anaconda/lib/site_perl/5.26.2 /home/fragua/anaconda/lib/5.26.2/x86_64-linux-thread-multi /home/fragua/anaconda/lib/5.26.2 .) at /home/fragua/RM/RepeatMasker/Taxonomy.pm line 80.
BEGIN failed--compilation aborted at /home/fragua/RM/RepeatMasker/Taxonomy.pm line 80.
Compilation failed in require at ./RepeatMasker line 310.
BEGIN failed--compilation aborted at ./RepeatMasker line 310.

I installed RepeatMasker in another computer without problems, but I don't know why now I encontered this problem

perl • 108 views
ADD COMMENTlink modified 4 weeks ago by genomax67k • written 4 weeks ago by frida10

can you check where the Soundex.pm is installed. Is that path include in @INC ? (would be a bit weird not to be so, but wont hurt checking it anyways)

ADD REPLYlink written 4 weeks ago by lieven.sterck4.8k

I solved the problem. thank you anyway

ADD REPLYlink written 4 weeks ago by frida10

perhaps briefly explain how you solved it , might be useful for future reference (and/or other users encountering the same issue). thx

ADD REPLYlink written 4 weeks ago by lieven.sterck4.8k
1

there were two build of perl installed. One of them was in my PATH. So i Chosen this one and the I installed Text::Soundex using sudo cpan

ADD REPLYlink written 4 weeks ago by frida10
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