search

zhou-lab / biscuit

BISulfite-seq CUI Toolkit
Other
62 stars 24 forks source link

vcf2bed segmentation fault #22

Closed ZhenyuZ closed 5 years ago

ZhenyuZ commented 7 years ago

I followed the instructions to use biscuit 0.2.2.20170522 for alignment and so on using a 58GB TCGA WGBS file. I repeatedly got segmentation fault at vcf2bed step

biscuit vcf2bed -k 10 -t cg output.vcf.gz > output.cg.bed

job killed when the output is about 42Mb. I have tried small input and have no problems.

Btw, I assume I can chunk the input VCF to smaller ones and get the same result after merging the output. Could you confirm this?

chrisamiller commented 5 years ago

I'm also seeing this happen on a large subset of WGBS samples (perhaps 25%). I'm consistently getting segfaulting in the middle of vcf2bed runs on large pileup.vcf.gz files from the biscuit pipeline. I can provide example files (though they're quite large) if needed.

zwdzwd commented 5 years ago

I think a lot has been updated since last year. Could you provide me the version number of biscuit you are using? Thanks.

chrisamiller commented 5 years ago

I'm using version 0.2.2.20170522, which I see is not the latest release. I'll try the latest version, and I'll report back tomorrow

chrisamiller commented 5 years ago

New version seems to solve the problem - this can be resolved. Thanks!

ttriche commented 5 years ago

fwiw, if you use samblaster with biscuit, be absolutely certain to use a version later than 0.3.2

--t

On Wed, Oct 17, 2018 at 10:48 AM Chris Miller notifications@github.com wrote:

New version seems to solve the problem - this can be resolved. Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/zwdzwd/biscuit/issues/22#issuecomment-430658824, or mute the thread https://github.com/notifications/unsubscribe-auth/AAARIhldSIyVQ24KUlzVtCD-WcDf72qxks5ul0MngaJpZM4PJWqY .

zwdzwd commented 5 years ago

Thank you for getting back @chrisamiller . I am glad it worked!