error when running

Detection of Miniature Inverted Repeat Transposable Elements

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#2 error when running

Milestone: 1.0

Status: closed

Owner: nobody

Labels: None

Updated: 2017-03-31

Created: 2016-08-31

Creator: JuanC

Private: No

I'me getting errors when trying to run:

>> tic;do_MITE_detection('/home/juan/Downloads/possible_TE_sequences_4D.fasta','-genome','rice');runtime = toc;
Starting parallel pool (parpool) using the 'local' profile ... connected to 1 workers.
Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in detectMITE (line 34)
                    fprintf(fid,'>%d|%d|%d|%d\n',j,candidate_startPos{j}{i}(k),candidate_endPos{j}{i}(k),candidate_tsdLen{j}{i}(k));


Error in do_MITE_detection (line 141)
    detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
        ,p_FlankSeq_Len,genome,p_cpu);

or even with a file

~~~

data_file = fopen('/home/juan/Downloads/possible_TE_sequences_4D.fasta')

data_file =

tic;do_MITE_detection(data_file,'-genome','rice');runtime = toc;
Error using fgets
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in fastaread2 (line 7)
l = fgets(fid);

Error in detectMITE (line 10)
genomeData = fastaread2(data_file);

Error in do_MITE_detection (line 141)
detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
,p_FlankSeq_Len,genome,p_cpu);
~~~

Related

Discussion

JuanC - 2016-08-31

Now I'm getting

./cd-hit/cd-hit-est: /home/juan/Documents/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./cd-hit/cd-hit-est)

Enviado desde Outlookhttp://aka.ms/weboutlook

De: JuanC juanmas07@users.sf.net
Enviado: miércoles, 31 de agosto de 2016 05:03:59 p.m.
Para: Ticket 2
Asunto: [detectmite:tickets] #2 error when running

[tickets:#2]https://sourceforge.net/p/detectmite/tickets/2/ error when running

Status: open
Milestone: 1.0
Created: Wed Aug 31, 2016 05:03 PM UTC by JuanC
Last Updated: Wed Aug 31, 2016 05:03 PM UTC
Owner: nobody

I'me getting errors when trying to run:

tic;do_MITE_detection('/home/juan/Downloads/possible_TE_sequences_4D.fasta','-genome','rice');runtime = toc;
Starting parallel pool (parpool) using the 'local' profile ... connected to 1 workers.
Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in detectMITE (line 34)
fprintf(fid,'>%d|%d|%d|%d\n',j,candidate_startPos{j}{i}(k),candidate_endPos{j}{i}(k),candidate_tsdLen{j}{i}(k));

Error in do_MITE_detection (line 141)
detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
,p_FlankSeq_Len,genome,p_cpu);

or even with a file

data_file = fopen('/home/juan/Downloads/possible_TE_sequences_4D.fasta') data_file = 3 tic;do_MITE_detection(data_file,'-genome','rice');runtime = toc; Error using fgets Invalid file identifier. Use fopen to generate a valid file identifier. Error in fastaread2 (line 7) l = fgets(fid); Error in detectMITE (line 10) genomeData = fastaread2(data_file); Error in do_MITE_detection (line 141) detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen ,p_FlankSeq_Len,genome,p_cpu);

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Related

Tickets: #2
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Congting Ye - 2016-09-01
  
  Hi JuanC,
  
  Please make sure to follow the instructions on the wiki page to install the detectMITE.
  
  (1) Make a folder '/result' in the current working directory of MATLAB. Some temporary files will be generated in this folder
  
  (2) Before running detectMITE, you should install the cd-hit correctly.
  
  For the cd-hit issue, it's the environment problem of your computer. You can issue the following command at the linux prompt to check wether your computer has 'libstdc++.so.6' or not,
  
  $locate libstdc++.so.6
  
  Here is my case:
  
  ice@ice-HP-Z640-Workstation:~$ locate libstdc++.so.6
  /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6
  /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6.0.17
  /usr/lib/i386-linux-gnu/libstdc++.so.6
  /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
  /usr/share/gdb/auto-load/usr/lib/i386-linux-gnu/libstdc++.so.6.0.21-gdb.py
  /usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21-gdb.py
  
  After that, use the following command to make a soft link,
  $ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6
  
  Hope this works for you. In case this doesn't work, you should reinstall your gcc with a higher version.
  
  Congting Ye
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - JuanC - 2016-09-01
    
    Hi,
    
    in which folder do you create the link?
    
    Enviado desde Outlookhttp://aka.ms/weboutlook
    
    De: Congting Ye yec@users.sf.net
    Enviado: jueves, 01 de septiembre de 2016 07:15:24 a.m.
    Para: [detectmite:tickets]
    Asunto: [detectmite:tickets] Re: #2 error when running
    
    Hi JuanC,
    
    Please make sure to follow the instructions on the wiki page to install the detectMITE.
    
    (1) Make a folder '/result' in the current working directory of MATLAB. Some temporary files will be generated in this folder
    
    (2) Before running detectMITE, you should install the cd-hit correctly.
    
    For the cd-hit issue, it's the environment problem of your computer. You can issue the following command at the linux prompt to check wether your computer has 'libstdc++.so.6' or not,
    
    $locate libstdc++.so.6
    
    Here is my case:
    
    ice@ice-HP-Z640-Workstation:~$ locate libstdc++.so.6
    /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6
    /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6.0.17
    /usr/lib/i386-linux-gnu/libstdc++.so.6
    /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21
    /usr/lib/x86_64-linux-gnu/libstdc++.so.6
    /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
    /usr/share/gdb/auto-load/usr/lib/i386-linux-gnu/libstdc++.so.6.0.21-gdb.py
    /usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21-gdb.py
    
    After that, use the following command to make a soft link,
    $ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6
    
    Hope this works for you. In case this doesn't work, you should reinstall your gcc with a higher version.
    
    Congting Ye
    
    [tickets:#2]https://sourceforge.net/p/detectmite/tickets/2/ error when running
    
    Status: open
    Milestone: 1.0
    Created: Wed Aug 31, 2016 05:03 PM UTC by JuanC
    Last Updated: Wed Aug 31, 2016 05:03 PM UTC
    Owner: nobody
    
    I'me getting errors when trying to run:
    
    tic;do_MITE_detection('/home/juan/Downloads/possible_TE_sequences_4D.fasta','-genome','rice');runtime = toc;
    Starting parallel pool (parpool) using the 'local' profile ... connected to 1 workers.
    Error using fprintf
    Invalid file identifier. Use fopen to generate a valid file identifier.
    
    Error in detectMITE (line 34)
    fprintf(fid,'>%d|%d|%d|%d\n',j,candidate_startPos{j}{i}(k),candidate_endPos{j}{i}(k),candidate_tsdLen{j}{i}(k));
    
    Error in do_MITE_detection (line 141)
    detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
    ,p_FlankSeq_Len,genome,p_cpu);
    
    or even with a file
    
    data_file = fopen('/home/juan/Downloads/possible_TE_sequences_4D.fasta') data_file = 3 tic;do_MITE_detection(data_file,'-genome','rice');runtime = toc; Error using fgets Invalid file identifier. Use fopen to generate a valid file identifier. Error in fastaread2 (line 7) l = fgets(fid); Error in detectMITE (line 10) genomeData = fastaread2(data_file); Error in do_MITE_detection (line 141) detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen ,p_FlankSeq_Len,genome,p_cpu);
    
    Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/detectmite/tickets/2/
    
    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
    
    Related
    
    Tickets: #2
    
    alternate
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
    - JuanC - 2016-09-01
      
      I was able to correct it changing the lib in the matlab folder.
      
      Now I'm getting another error:
      
      Apprixmated maximum memory consumption: 48M
      writing new database
      writing clustering information
      program completed !
      
      Total CPU time 0.04
      Error using fastaread (line 158)
      Input does not exist or is not a valid FASTA file.
      
      Error in detectMITE (line 60)
      Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count)
      '.fasta.clstr']);
      
      Error in do_MITE_detection (line 141)
      detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
      ,p_FlankSeq_Len,genome,p_cpu);
      
      looking forward to see the results!
      
      thank you
      
      Enviado desde Outlookhttp://aka.ms/weboutlook
      
      De: Juan M. Crescente juanma_lace@hotmail.com
      Enviado: jueves, 01 de septiembre de 2016 01:04 p.m.
      Para: [detectmite:tickets]
      Asunto: Re: [detectmite:tickets] Re: #2 error when running
      
      Hi,
      
      in which folder do you create the link?
      
      Enviado desde Outlookhttp://aka.ms/weboutlook
      
      De: Congting Ye yec@users.sf.net
      Enviado: jueves, 01 de septiembre de 2016 07:15:24 a.m.
      Para: [detectmite:tickets]
      Asunto: [detectmite:tickets] Re: #2 error when running
      
      Hi JuanC,
      
      Please make sure to follow the instructions on the wiki page to install the detectMITE.
      
      (1) Make a folder '/result' in the current working directory of MATLAB. Some temporary files will be generated in this folder
      
      (2) Before running detectMITE, you should install the cd-hit correctly.
      
      For the cd-hit issue, it's the environment problem of your computer. You can issue the following command at the linux prompt to check wether your computer has 'libstdc++.so.6' or not,
      
      $locate libstdc++.so.6
      
      Here is my case:
      
      ice@ice-HP-Z640-Workstation:~$ locate libstdc++.so.6
      /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6
      /home/ice/Programs/MATLAB/sys/os/glnxa64/libstdc++.so.6.0.17
      /usr/lib/i386-linux-gnu/libstdc++.so.6
      /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21
      /usr/lib/x86_64-linux-gnu/libstdc++.so.6
      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
      /usr/share/gdb/auto-load/usr/lib/i386-linux-gnu/libstdc++.so.6.0.21-gdb.py
      /usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21-gdb.py
      
      After that, use the following command to make a soft link,
      $ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 libstdc++.so.6
      
      Hope this works for you. In case this doesn't work, you should reinstall your gcc with a higher version.
      
      Congting Ye
      
      [tickets:#2]https://sourceforge.net/p/detectmite/tickets/2/ error when running
      
      Status: open
      Milestone: 1.0
      Created: Wed Aug 31, 2016 05:03 PM UTC by JuanC
      Last Updated: Wed Aug 31, 2016 05:03 PM UTC
      Owner: nobody
      
      I'me getting errors when trying to run:
      
      tic;do_MITE_detection('/home/juan/Downloads/possible_TE_sequences_4D.fasta','-genome','rice');runtime = toc;
      Starting parallel pool (parpool) using the 'local' profile ... connected to 1 workers.
      Error using fprintf
      Invalid file identifier. Use fopen to generate a valid file identifier.
      
      Error in detectMITE (line 34)
      fprintf(fid,'>%d|%d|%d|%d\n',j,candidate_startPos{j}{i}(k),candidate_endPos{j}{i}(k),candidate_tsdLen{j}{i}(k));
      
      Error in do_MITE_detection (line 141)
      detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
      ,p_FlankSeq_Len,genome,p_cpu);
      
      or even with a file
      
      data_file = fopen('/home/juan/Downloads/possible_TE_sequences_4D.fasta') data_file = 3 tic;do_MITE_detection(data_file,'-genome','rice');runtime = toc; Error using fgets Invalid file identifier. Use fopen to generate a valid file identifier. Error in fastaread2 (line 7) l = fgets(fid); Error in detectMITE (line 10) genomeData = fastaread2(data_file); Error in do_MITE_detection (line 141) detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen ,p_FlankSeq_Len,genome,p_cpu);
      
      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/detectmite/tickets/2/
      
      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
      
      Related
      
      Tickets: #2
      
      alternate
      
      If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
      - Congting Ye - 2016-09-01
        
        It seems like your cd-hit didn't run correctly, and cd-hit didn't generate cluster file which caused the error 'Input does not exist or is not a valid FASTA file.'
        
        If there is any memory limitation of using cd-hit?
        
        Congting Ye
        
        If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Congting Ye - 2017-03-31

status: open --> closed
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