Activity for detectMITE
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Auriel Xue created ticket #4
error when running
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Virginia Markham posted a comment on ticket #3
Hm okay, I'll try that. Thanks!!
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Congting Ye posted a comment on ticket #3
In your case, this indicates that no candidate MITEs was detected from your input. I guess that you may run detectMITE using a small fasta file for test, a small input often results in nothing detected. You could run detectMITE with Arabidopsis genome to test whether it could run correctly. Thanks for your interest in detectMITE!
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Thanks so much for your response! Sorry, I should have been more clear. This is my first time posting on sourceforge, apologies for my mistakes. That error you mention ( "Cluster = fastaread(['./result/' ...") is from Juan C. I did not get that error. In fact, I did not get any error message at all. But like Juan C., only my first few iterations are giving clusters. I have 15 iterations and the first 8 look good (for example: "80597 finished 51831 clusters"), but the last 7 are not giving results...
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Thanks so much for your response! Sorry, I should have been more clear. This is my first time posting on sourceforge, apologies for my mistakes. That error you mention ( "Cluster = fastaread(['./result/' ...") is from Juan C. I did not get that error. In fact, I did not get any error message at all. But like Juan C., only my first few iterations are giving clusters. I have 15 iterations and the first 8 look good (for example: "80597 finished 51831 clusters"), but the last 7 are not giving results...
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Thanks so much for your response! Sorry, I should have been more clear. This is my first time posting on sourceforge, apologies for my mistakes. That error you mention ( "Cluster = fastaread(['./result/' ...") is from Juan C. I did not get that error. In fact, I did not get any error message at all. But like Juan C., only my first few iterations are giving clusters. I have 15 iterations and the first 8 look good (for example: "80597 finished 51831 clusters"), but the last 7 are not giving results...
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Thanks so much for your response! Sorry, I should have been more clear. This is my first time posting on sourceforge, apologies for my mistakes. That error you mention ( "Cluster = fastaread(['./result/' ...") is from Juan C. I did not get that error. In fact, I did not get any error message at all. But like Juan C., only my first few iterations are giving clusters. I have 15 iterations and the first 8 look good (for example: "80597 finished 51831 clusters"), but the last 7 are not giving results...
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Hi Virginia Markham, According to the error info you post, I figure out that you were using an old version of detectMITE. The code "Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count) '.fasta.clstr']);" is at line 60 of the old verion (such as detectMITE.20160818.tar.gz), but at line 62 of the newest version. Please go the link (https://sourceforge.net/projects/detectmite/files/detectMITE.20170425.tar.gz/download) to download the newest version. Error using fastaread (line...
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Hi, I'm still getting this error even though I'm quite sure I'm using the newest version of detectMITE. It gives results for only the first 8 out of 15 iterations. Any idea what the problem might be? Thanks!! I'm running this on our server which is SUSE Linux Enterprise Server 12 SP3, and I'm using Matlab version R2016a and cd-hit v4.6.1-2012-08-27.
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Tim Amos posted a comment on discussion General Discussion
FYI if you've got a problem with the program you could try submitting an issue under the "Tickets" tab. The developers appear to have answered those.
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Error when running
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shengweima posted a comment on discussion General Discussion
Apprixmated maximum memory consumption: 481M writing new database writing clustering information program completed ! Total CPU time 80287.80 Index exceeds matrix dimensions. Error in detectMITE (line 123) Sequence = genomeData(Number).Sequence(startPos:endPos); 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); IdleTimeout has been reached. Parallel pool using the 'local' profile is shutting...
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UpdateHistory
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User Manual
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detectMITE released /detectMITE.20170425.tar.gz
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error when running
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Hello JuanC, The error is produced when some temporary file is empty (means no candidate...
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User Manual
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UpdateHistory
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JuanC modified a comment on ticket #3
It seems like it is iterating through 8 candidates but from 4th on they are empty...
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It seems like it is iterating through 8 candidates but the from 4th on they are empty...
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Content of one of the clstr file. >Cluster 0 0 149nt, >129|252|400|2... * >Cluster...
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Error when running
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User Manual
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User Manual
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It seems like your cd-hit didn't run correctly, and cd-hit didn't generate cluster...
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I was able to correct it changing the lib in the matlab folder. Now I'm getting another...
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Hi, in which folder do you create the link? Enviado desde Outlookhttp://aka.ms/weboutlook...
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Hi JuanC, Please make sure to follow the instructions on the wiki page to install...
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Now I'm getting ./cd-hit/cd-hit-est: /home/juan/Documents/matlab/sys/os/glnxa64/libstdc++.so.6:...
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error when running
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UpdateHistory
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Problem with detectMITE
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parpool is a function in the 'Parallel Computing Toolkit', which is an optional toolkit...
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Felipe Marques de Almeida created ticket #1
Problem with detectMITE
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User Manual
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User Manual
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UpdateHistory
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UpdateHistory
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UpdateHistory
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UpdateHistory
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User Manual
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User Manual
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User Manual
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User Manual
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User Manual
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[Q1]: Why does detectMITE identify much larger number of MITE families than the ones produced by other tools or database?
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User Manual
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User Manual
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User Manual
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[Q2]: What does the description line mean in the output (in FASTA format) of detectMITE?
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[Q2]: What does the description line mean in the output (in FASTA format) of detectMITE?
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[Q2]: What does the description line mean in the output (in FASTA format) of detectMITE?
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[Q1]: Why does detectMITE identify much larger number of MITE families than the ones produced by other tools or database?
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[Q1]: Why does detectMITE identify much larger number of MITE families than the ones produced by other tools or data base?
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