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Bedops Gtf2Bed Function Throws Error: Unable To Access --Max-Mem

Hello, I am trying to convert genes.gtf to genes.bed with gtf2bed from bedops. 

gtf2bed < genes.gtf >genes.bed

But, it stopped with the message: "Unable to access --max-mem", anyone has similar quesitions?

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updated by Ashutosh Pandey Ashutosh Pandey • written by Frewise • Frewise

I have edited the title so that Alex Reynolds can easily find this post. He is the author of BEDOPS.

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written by Ashutosh Pandey Ashutosh Pandey

I don't have much to go on here, so if you can add some details, that would be very helpful. What versions of Python and BEDOPS are you running (and on what platform), and can you post your GTF file somewhere public for me to test on this end? Can you also post a full transcript of the error message?

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written by Alex Reynolds Alex Reynolds

1 answer

The default "--max-mem" parameter for sorting bed file is 2Gb. It seems that your system has less RAM than 2Gb. You can use this parameter to specify how much RAM you want to devote for sorting purpose. Try

gtf2bed --max-mem 1G < genes.gtf >genes.bed

or

gtf2bed --max-mem 500M < genes.gtf >genes.bed

Additionally, you can use "--do-not-sort" option if you don't want to sort your bed file that will be created from the gtf file.

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written by Ashutosh Pandey Ashutosh Pandey

Thanks for your edition and suggestion. My free RAM is more than 26G now, and I modified the value of "--max-mem" and tried the "--do-not-sort" parameter, but return the same error.

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written by Frewise • Frewise

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