segmentation fault on quantification

[aswathyseb]

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]

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

[kspham]

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

[aswathyseb]

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

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On 4 September 2017 at 17:29, Son Pham ***@***.***> 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 <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFH-L7FW2jglGDexZMRTvlBMNElx2yQRks5sfGvQgaJpZM4PKZRG> .

[bioturing]

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

…

On Tue, Sep 5, 2017 at 7:03 AM, Aswathy ***@***.***> 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 ***@***.***> 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 > <#14 (comment)>, 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 <#14 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AdEcJCzHzbTPG4X8d4pOeKHlmzAgUNKsks5sfVTIgaJpZM4PKZRG> .

[kspham]

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

[aswathyseb]

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]

Hi,

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

Thanks,
Aswathy