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bioturing / hera

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segmentation fault on quantification #14

Open aswathyseb opened 7 years ago

aswathyseb commented 7 years ago

Hello,

We ran hera on our samples and we get "segmentation fault" for the quantification of one of our samples. Below is the command I ran and the error message that I get.

hera quant -i /export/refs/hera/GRCh38 ../TS.fq.gz -p TS Hera is a program developed by BioTuring for RNA-Seq analysis. Please contact info@bioturing.com if you need further support Number of aligned readsd: 41598442/45288011
Mean read lenght : 99.672771 Running EM ... Segmentation fault

I tried the same command with -f option and it is generating bam file. I can send you the bam file if needed. Thanks,

kspham commented 7 years ago

Hi Aswathy, Can you provide me the fastq.gz file so that we can try to reproduce the error? Thank you!

kspham commented 7 years ago

Also, it would be helpful to know which version of hera that you ran!

aswathyseb commented 7 years ago

Hello Son,

Thank you for getting back to me. I am using hera - v1.0.1

Here is the link to the fastq file that gives me the 'segmentation fault' error.

https://drive.google.com/open?id=0B8Mg3kF0hu9DRFpZRnFzd3p0Tnc

Thanks, Aswathy

On 4 September 2017 at 17:29, Son Pham notifications@github.com wrote:

Also, it would be helpful to know which version of hera that you ran!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bioturing/hera/issues/14#issuecomment-327030299, or mute the thread https://github.com/notifications/unsubscribe-auth/AFH-L7FW2jglGDexZMRTvlBMNElx2yQRks5sfGvQgaJpZM4PKZRG .

bioturing commented 7 years ago

Thanks, Aswathy! We already got the file and will get back soon.

On Tue, Sep 5, 2017 at 7:03 AM, Aswathy notifications@github.com wrote:

Hello Son,

Thank you for getting back to me. I am using hera - v1.0.1

Here is the link to the fastq file that gives me the 'segmentation fault' error.

https://drive.google.com/open?id=0B8Mg3kF0hu9DRFpZRnFzd3p0Tnc

Thanks, Aswathy

On 4 September 2017 at 17:29, Son Pham notifications@github.com wrote:

Also, it would be helpful to know which version of hera that you ran!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bioturing/hera/issues/14#issuecomment-327030299, or mute the thread https://github.com/notifications/unsubscribe-auth/AFH- L7FW2jglGDexZMRTvlBMNElx2yQRks5sfGvQgaJpZM4PKZRG .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bioturing/hera/issues/14#issuecomment-327185226, or mute the thread https://github.com/notifications/unsubscribe-auth/AdEcJCzHzbTPG4X8d4pOeKHlmzAgUNKsks5sfVTIgaJpZM4PKZRG .

kspham commented 7 years ago

Very interesting --- can you tell me what is the memory you have? We somehow can not get a segfault for your file :)

aswathyseb commented 7 years ago

We ran it on a high memory linux machine(500GB). I see that you have a new version of hera and I am trying to run the latest version now.

aswathyseb commented 7 years ago

Hi,

I could run hera quant on this sample successfully on this sample using v1.1.

Thanks, Aswathy