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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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Unable to run create-profmark.c #281

Closed wolf-Peng closed 1 year ago

wolf-Peng commented 2 years ago

Hi,

I am trying to use create-promark.c to create a new training-test set of dna. I excuted ./create-profmark pmark sequence.stockholm sequence.fa where sequence.stockholm was generated by mafft from sequence.fa. And it raise an error: Failed to open SSI index file

Could you help me solve it? Thank you

cryptogenomicon commented 2 years ago

Both the MSA and sequence file need to be indexed for fast sequence lookup and retrieval; we call these index files "SSI" files. The program to create them are esl-afetch and esl-sfetch in the Easel tools that come with HMMER in the easel subdirectory of its source code.

    % esl-afetch --index <msafile>
    % esl-sfetch --index <fastafile>
npcarter commented 2 years ago

Also, we plan to make this error message more informative in the next release, as a number of people have had the same issue that you did. -Nick

On Fri, Jun 10, 2022 at 1:34 AM wolf-Peng @.***> wrote:

Hi,

I am trying to use create-promark.c to create a new training-test set of dna. I excuted ./create-profmark pmark sequence.stockholm sequence.fa where sequence.stockholm was generated by mafft from sequence.fa. And it raise an error: Failed to open SSI index file

Could you help me solve it? Thank you

— Reply to this email directly, view it on GitHub https://github.com/EddyRivasLab/hmmer/issues/281, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDJBZAMM5VHQ34YJQSXSL3VOLHW7ANCNFSM5YMOXYJA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

wolf-Peng commented 2 years ago

hello, I want to use the develop version of create_profmark and I run the command: git clone https://github.com/EddyRivasLab/hmmer cd hmmer git clone https://github.com/EddyRivasLab/easel git checkout develop autoconf ./configure make Then it raised an error esl_sq.c: In function ‘esl_sq_BlockReallocSequences’: esl_sq.c:611:3: error: ‘for’ loop initial declarations are only allowed in C99 mode for(int i = 0; i < block->listSize; i++){ ^ esl_sq.c:611:3: note: use option -std=c99 or -std=gnu99 to compile your code make[1]: *** [esl_sq.o] Error 1 make: *** [all] Error 2 How to change it to C99 mode? Thank you. @cryptogenomicon