Entering edit mode
3.5 years ago
fernandogs97
▴
30
Good afternoon, I'm doing a series of mappings on human RNA-seq samples. I have a computer with 60 GB of RAM and 8 cores. When mapping the samples with the gtf file and the genome index I always get the following error:
/home/alba/STAR-2.7.6a/bin/Linux_x86_64/STAR --runThreadN 5 --genomeDir /home/alba/Desktop/TFM_Fernando_Gálvez/Análisis/index/Human/STAR/hg38/genomeDir --readFilesIn /home/alba/Desktop/TFM_Fernando_Gálvez/Análisis/reanchino/rawdata/SRR6267334/SRR6267334.fastq
May 26 12:20:52 ..... started STAR run
May 26 12:20:52 ..... loading genome
May 26 12:21:00 ..... started mapping
Segmentation fault (core dumped)
I've been testing different solutions to this problems, I think that I shouldn't have this problem as the RAM of my computer is theoretically sufficient for this analysis. Thanks in advance to anyone that can help me with this problem.
It has been seen that in many applications, increasing the number is threads also increases the amount of memory utilised. Try the default command without using "--runThreadN" and see what happens. Or, you can also set it to 1 (unless that is the default).
Thank you very much for your help but I've just tried it and it the error is still there...
STAR is actually infamous for utilising a lot of memory (not sure if this has been taken care in its latest releases). Please go through this post: STAR alignment killed. Try keeping a track of how much memory is STAR utlising. May be 60 GB is not enough for your run.
Thank you for sharing the post, for testing that I have been analyzing the consumption of the RAM during the analysis and it does not exceed 30 GB of RAm at any time
Did you download pre-compiled STAR or compile it yourself? Is your copy known to work? Did you make the indexes yourself?
I pre-compiled a known version of STAR and in others computers of my lab it works without problems.
Then next thing would be to try to look at the indexes and re-make them if necessary. Check to make sure your input files are in correct format.
The latest release version is 2.7.9a. You should update first and see if the problem persists. If the problem persists, generate a reduced test set from e.g. one chromosome only and possibly also a small fastq file.