Cufflinks 2 Problem: No Output Files
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12.0 years ago

Hi,

After tophat 2.0.0.1 ran on my samples, I tried cufflinks 2.0 on them. All cufflinks job worked well except on one of my samples. In the output directory, there is no files. and when I watch in the log file, there is no error. cufflinks is still running when I do a top but in the log file it seems that cufflinks has stopped ( it stopped at this line ... )

Processing Locus Chr1:98338724-98338989 [ ] 3%

Anybody has an idea to resolve this problem ?

Thanks,

N.

cufflinks • 3.9k views
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Can you provide more information? like the difference among the sample data? This one is bigger? Did you run on cluster or just one PC/node?

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Yes indeed it's the the biggest sample ( ~8 Gb bam file from tophat2) . And yes it's on a cluster. I tried with 20Gb of memory with no results ...

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Hi Nicobxl, did you solve your problem? I'm currently facing a very similar one, I mean, I'm getting stats (FPKM) on some of my samples but not on other. However they have been analyzed according to the same pipeline, at the same time...

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hello,did you solve the problem? I have the same problem,so are you solving the problem?

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It was a memory problem. Try using more RAM and use less threads

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or try another tool like STAR

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Thank you for your help ! And i want to know STAR means what ? Could you please tell me the website?

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STAR is a splice-aware aligner like tophat, but much more faster and in my experience perform better alignment than tophat. Here's the code : https://code.google.com/p/rna-star/ , the paper : http://www.ncbi.nlm.nih.gov/pubmed/23104886 and the google group for question : https://groups.google.com/d/forum/rna-star The only problem with STAR is that it used more RAM, but it's way more faster !

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Thank you very much,it's very useful to me!

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