Core Dumped - STAR mapping
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4 months ago

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 12:21:00 ..... 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.

RNA-seq human STAR • 389 views
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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).

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Thank you very much for your help but I've just tried it and it the error is still there...

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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.

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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

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Did you download pre-compiled STAR or compile it yourself? Is your copy known to work? Did you make the indexes yourself?

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I pre-compiled a known version of STAR and in others computers of my lab it works without problems.

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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.

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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.