featureCounts

Question

[kcarey]

Hey Guys, I have been trying to run this code to generate counts data using featureCounts Subread package on my server:

featureCounts -p -T 20 -a gencode.v36.chr_patch_hapl_scaff.annotation.gtf -g 'gene_id' -o ../Matched/Counts/readCounts.txt ../Matched/*.bam

And it is generating temporary files (see attached)....not creating the appropriate text file. Can you provide some insight into this error? I am not sure if it is a server issue or something I am missing...

I keep getting this message of "core dump" and not the completed count file...

Answer 1

[ATpoint]

The tmp files are normal and expected during the counting process. The segmentation fault could indicate a memory shortage. On which type or machine do you run it and what are its specs?

[kcarey]

Thank you for your response. Oh okay, I am running it on a server and it has 20 cores. I ran all 20....and since it seemed overloaded I decreased them (* in the code this is T 20). but it still kept giving me that error....so its not a code issue?

Im am attempting to ask for help from the institution housing the server. I am a graduate student.

[ATpoint]

The segmentation fault could indicate a memory shortage

On which type or machine do you run it and what are its specs?

As said, it's likely a memory error. So, how much is available, and how much did you request? Is this a server that has a scheduler such as SLURM?

[kcarey]

We have 363 G and only 32 G was used, also ran htop while running in another tab and did see it is not using much memory....I. believe the crashing is a featureCounts error....also added more to code....I did not specify 'abc.txt' at the end of my code by the -o...also believe the annotation file was not correct, I used Gh37 build and the version of annotation was for 38....going to try with Gh37 annotation file from gencode now (https://www.gencodegenes.org/human/release_40lift37.html) please let me know if you have any other recommendations.

I appreciate your help.