Author Topic: Error in gtf2bed  (Read 5072 times)

zebasilio

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Error in gtf2bed
« on: February 14, 2017, 12:44:39 AM »
Hi

I am trying to convert a gtf to a bed file but I am always getting this error message:

$gtf2bed < genes.gtf > genes.gtf.bed

*** Error in `convert2bed': realloc(): invalid next size: 0x0000000001337f60 ***
/home/jose/bin/gtf2bed: line 122: 16784 Aborted                 (core dumped) ${cmd} ${options} - 0<&0

I am using version:  2.4.24

Thanks for your help. Josť

AlexReynolds

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Re: Error in gtf2bed
« Reply #1 on: February 14, 2017, 01:27:24 AM »
Can you please send me a copy of your GTF file? (If you can post it publicly.) Also, can you please describe your host environment? Thanks!

zebasilio

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Re: Error in gtf2bed
« Reply #2 on: February 15, 2017, 03:26:56 AM »
Dear Alex,

The gtf file is from a igenome mouse annotation : https://drive.google.com/open?id=0BwFH7GVC19-NbDNhWkl1R1dfVVU .The remaining requested info are in the attached files

Thank you,
Josť

AlexReynolds

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Re: Error in gtf2bed
« Reply #3 on: February 15, 2017, 10:01:01 PM »
Thanks! I'm away for a couple weeks, but I will investigate when I get back. I have a ticket here where you can follow any future commits/patches to this issue: https://github.com/bedops/bedops/issues/174