Closed wolf-Peng closed 1 year 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>
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
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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
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