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

Question

[Frewise]

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?

[Ashutosh Pandey]

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

[Alex Reynolds]

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?

Answer 1

[Ashutosh Pandey]

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.

[Frewise]

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.

[Ashutosh Pandey]

I found this link http://ea-utils.googlecode.com/svn/trunk/clipper/gtf2bed