bds: Received OS signal 'hangup'

[xuguorong2016]

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]

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]

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]

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

[biomystery]

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: [email protected] [email protected] Linkedin: www.linkedin.com/in/biomystery/

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[xuguorong2016]

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!