Dear members,
I am trying to use Tophat, but it keeps failing with error -1: can not retrieve sequence XXXX from stream. Initially, I though there was some problem with the cluster I was running the analysis on. Because of the error mentioned "stream" I was suspecting of memory error, although I have more than 24GB of RAM per node. Thus, I did a test run in another cluster, and got the very same error. Well, if I run the analysis only using one thread the problem seems to resolve, however this is VERY time consuming and I have a lot of samples to analyze.
So, my suspicions is that I am seeing some bug while processing colorspace data in multiple threads.
I am wondering if any one has seem this problem and know a practical solution for that. Since it seems to be a coding problem I am not sure that there is any easy solution. So, I am wondering if someone has experience with another RNA-Seq analysis pipelines that does not involve Tophat, and could point me to some software alternatives/pipelines.
Thank you.
Lucas
I am trying to use Tophat, but it keeps failing with error -1: can not retrieve sequence XXXX from stream. Initially, I though there was some problem with the cluster I was running the analysis on. Because of the error mentioned "stream" I was suspecting of memory error, although I have more than 24GB of RAM per node. Thus, I did a test run in another cluster, and got the very same error. Well, if I run the analysis only using one thread the problem seems to resolve, however this is VERY time consuming and I have a lot of samples to analyze.
So, my suspicions is that I am seeing some bug while processing colorspace data in multiple threads.
I am wondering if any one has seem this problem and know a practical solution for that. Since it seems to be a coding problem I am not sure that there is any easy solution. So, I am wondering if someone has experience with another RNA-Seq analysis pipelines that does not involve Tophat, and could point me to some software alternatives/pipelines.
Thank you.
Lucas
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