Question: Segmentation failed (core dumped) error in featureCounts
0
gravatar for Batu
6 months ago by
Batu110
Batu110 wrote:

Hello,

When I run featureCounts, it gives an error after loading GTF file and showing number of chromosomes.

    featureCounts -T 3 -t exon -g gene_id -a "/mnt/c/Users/user/Desktop/STEMCELL/RNA_3/References/Homo_sapiens.GRCh38.92.gtf" -o "/mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Output_Files/SRR1639080_readCounts.txt" "/mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Output_Files/SRR1639080_sorted.bam"

Output is below:

        ==========     _____ _    _ ____  _____  ______          _____
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
          v1.6.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           S /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/O ... ||
||                                                                            ||
||             Output file : /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Out ... ||
||                 Summary : /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Out ... ||
||              Annotation : /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Ref ... ||
||      Dir for temp files : /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Out ... ||
||                                                                            ||
||                 Threads : 3                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file /mnt/c/Users/user/Desktop/STEMCELL/RNA_3/Referenc ... ||
||    Features : 1237303                                                      ||
||    Meta-features : 58395                                                   ||
||    Chromosomes/contigs : 47                                                ||
||                                                                            ||
Segmentation fault (core dumped)

I couldn't find anything specific for featureCounts. But in the posts, it is generally said that "Segmentation fault" means that you tried to access memory that you do not have access to. I couldn't resolve how I can resolve it.

Any ideas or suggestions? Thanks...

ADD COMMENTlink modified 5 months ago • written 6 months ago by Batu110
1

I've occasionally run into segfaults with featureCounts and found that switching versions (typically to the newest one) tends to resolve this.

ADD REPLYlink written 6 months ago by Devon Ryan87k

Switching with 1.6.2 did not resolve the problem

ADD REPLYlink written 6 months ago by Batu110
1
gravatar for Batu
5 months ago by
Batu110
Batu110 wrote:

Workaround for this problem is to recompile subread package with the recent glibc (https://github.com/Microsoft/WSL/issues/3391). To do that, update glibc to the newest version (2.23), and then compile the source of the package, and introduce its "bin" directory to path. Problem solved!!

ADD COMMENTlink modified 5 months ago • written 5 months ago by Batu110
1
gravatar for ATpoint
6 months ago by
ATpoint12k
Germany
ATpoint12k wrote:

How much memory do you have available?

ADD COMMENTlink written 6 months ago by ATpoint12k

I have 8GB RAM on my PC

ADD REPLYlink written 6 months ago by Batu110

I've tried the same code in another PC with 16GB of memory, and it worked seamlessly. So the problem was the memory. Thanks for your help!!

ADD REPLYlink written 6 months ago by Batu110

Good to hear it worked. Please consider to mark the answer as accepted to help others in the future.

ADD REPLYlink written 6 months ago by ATpoint12k

My friend tried featureCounts on a computer with much higher RAM, but she got the same error. When I solved the problem, I tried on computer with Ubuntu. But me and my friend are using Ubuntu in Windows (WSL). Can this be a reason? How and why this problem occurs? Any idea? Thanks...

ADD REPLYlink written 6 months ago by Batu110
1

Hard to say, upload the files to a public Galaxy server and try there. That'll be using a regular linux server to run things.

ADD REPLYlink written 6 months ago by Devon Ryan87k

It does not matter how much RAM the host computer has, but how much is allocated to the virtual machine. Check how much is indeed consumable for the VM.

ADD REPLYlink written 6 months ago by ATpoint12k

Actually, WSL is not a virtual machine. It is a subsystem in Windows and works almost natively (almost, because I had an error). I saw that there was a bug that restricts the usage of RAM on WSL 2 years ago, but now it is fixed and I can see all amount of RAM there.

ADD REPLYlink written 6 months ago by Batu110
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