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bcgsc / Trans-NanoSim

Oxford nanopore transcriptome read simulator
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Segmentation Fault error #1

Closed ddurai closed 5 years ago

ddurai commented 6 years ago

Hi, I am very interested in using the code for simulating RNA oxford nanopore reads. But when I run the code I always encounter a segmentation fault. I am using a system with all the required softwares and libraries installed and a python whose version is 3.6.1. Can you please help me in fixing this issue

Thanks

regards Dilip

cheny19 commented 6 years ago

Hi Dilip,

Could you provide the log file including the error you encountered? If possible, please also point me the input files you used when the seg fault occured. So I can try to figure out that's causing the error and debug.

Thanks, Chen

SaberHQ commented 5 years ago

Hi @ddurai Would you please copy paste the error so that I can see where it happens?

ddurai commented 5 years ago

Dear @SaberHQ and @cheny19 Thank you for your reply and I apologise for the delay in responding. I do not get any log file. All I get is a segmentation fault within 2 minutes of my execution. Here is the command I am using:

python read_analysis.py /input/K562.fq -rg hg38.fa -rt Homo_sapiens.GRCh38.cdna.all.fa -annot Homo_sapiens.GRCh38.93.gtf

Unfortunately, I will not be able to provide you with the original fastq file I have as it is currently unpublised. I have attached the screenshot of my execution with this msg

Regards Dilip ScreenTransNanoSim.pdf

SaberHQ commented 5 years ago

Dear @ddurai

I was actually working on incorporating this pipeline within the NanoSim repo. The work is done and you may now use it to simulate both genomic and transcriptomic reads! This repo is now deprecated.

I do believe that Segmentation Fault is something related to your own workstation's memory. Please try our new pipeline in a new computer and see if it solves the issue. I am closing the issue, you may use NanoSim pipeline now as this repo is deprecated.