Entering edit mode
11.9 years ago
Nicolas Rosewick
10k
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.
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?
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 ...
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...
hello,did you solve the problem? I have the same problem,so are you solving the problem?
It was a memory problem. Try using more RAM and use less threads
or try another tool like STAR
Thank you for your help ! And i want to know STAR means what ? Could you please tell me the website?
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 !
Thank you very much,it's very useful to me!