Sabre demultiplexer
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2.1 years ago
mropri ▴ 150

I am running sabre to try to demultiplex my rna-seq data. I run the command:

sabre pe -f round05_rep1_R1.fastq.gz -r round05_rep1_R2.fastq.gz -b drs_round05_rep1_sabre.tsv -u unknown_bar1.fastq -w unknown_bar2.fastq

However, I get a segmentation error with a core dump. My barcode file has 3 columns, the well number, the read sequence, and the barcode. I do not understand why I am getting this error. Any help is appreciated.

demultiplexing Sabre RNA-seq • 1.4k views
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Hi, I am having the same error with an 81gb file. I am working on a ubuntu server. What did you mean by upping the memory? I was originally using a different server and switched to one with 1 terabyte of memory and I am still getting the message segmentation Fault (core dumped). Any help would be much appreciated!!

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Random access memory (RAM) is not the same thing as storage. If you actually have a TB of RAM then demultiplexing a 81G file should not be a problem. Is this a standalone server? If others are using the server at the same time then you may still have a much smaller amount of RAM available to your job.

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2.1 years ago
GenoMax 144k

Are these particularly large sequence files? One problem may be simply running out of available memory.

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its 122 GB, let me try upping the memory.

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memory was the problem, it worked fine as I upped the memory. Thank you

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