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epigen-UCSD / atac_seq_pipeline

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bds: Received OS signal 'hangup' #15

Open xuguorong2016 opened 5 years ago

xuguorong2016 commented 5 years ago

Hello,

I am recently using your pipeline with two replicates but keeping having the hangup issue during the alignment stage, do you have any suggestions?

2019/05/29 16:24:49 bds: Received OS signal 'hangup' 2019/05/29 16:24:49 Info: Killing PID '37373'

What log files do you need to figure out the issue?

Thanks!

biomystery commented 5 years ago

Can you provide:

  1. is it running on TSCC or your local machine?
  2. if it is tscc, can you provide you qsub script ?
  3. Can you provide the atac.bds.xxx.report.html and/or log from tscc?
xuguorong2016 commented 5 years ago

Thanks for your response! It is running on my local machine. Please see the attached report html. atac.bds.20190529_140346_194.report.html.zip

xuguorong2016 commented 5 years ago

Hi Frank, Do you have any suggestions about how to fix this issue? Thanks!

biomystery commented 5 years ago

Hi Guorong,

You can either try:

  1. Re-run the job again. The pipeline will pick up from where it stopped automatically.
  2. I would suggest you try tp run these libraries separately. You now run them as rep1 and rep2 but I may have customized the pipeline for running each lib individually. Then do downstream analysis.

Let me know how it goes.

You can find me in person as well.

Best Frank

Zhang (Frank) Cheng Bioinformatics Scientist/Data Scientist Center for Epigenomics, UC San Diego https://healthsciences.ucsd.edu/som/cmm/research/epigenomics/pages/default.aspx office: 858-534-7351 cell: 858-412-7598 E-mail: zhangc518@gmail.com zhc268@ucsd.edu Linkedin: www.linkedin.com/in/biomystery/

On Mon, Jun 3, 2019 at 10:20 PM Guorong Xu notifications@github.com wrote:

Hi Frank, Do you have any suggestions about how to fix this issue? Thanks!

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xuguorong2016 commented 5 years ago

Hi Frank,

Thanks a lot for your response! When I reran the command the pipeline did not pickup the alignment automatically but it reran from the cutadapt. Do I need to set configuration to allow to pickup the stop point automatically?

Could you tell me where your customized pipeline or command examples to run sample individually and then combine together for downstream analysis?

Thanks!