Former User of DNAx Community_47

Interestingly, I found that this OOM error is only "masked" when the offending process is given as a process substitution file input.That is, when I do the command like the below, it may incorrectl...

• View comment
• 20 December 2023 00:51
• 0 votes

I realised that passing --get-streams to dx watch restricts the output to the stdout and stderr streams of the app, whereas if I omit this parameter (just dx watch jobid) then I get more detail, an...

• View comment
• 18 December 2023 23:01
• 0 votes

How to tell that a job has failed due to an out of memory error when it completes with state "done"

I am running an applet on the DNA Nexus RAP that pipes output from bcftools into another program. Sometimes the applet runs into insufficient memory... but it does not die with an error - it comple...

• Former User of DNAx Community_47
• 18 December 2023 00:00
• 2 followers
• 3 comments
• 0 votes

That's a good idea to try, thanks!

• View comment
• 02 December 2022 16:22
• 0 votes

DNA Nexus takes ages to run a job

The past week or more, it takes many hours before any job that I submit starts running on DNA Nexus. This makes it nearly impossible to develop / debug an app or commands I want to run. Does anyone...

• Former User of DNAx Community_47
• 02 December 2022 00:00
• 2 followers
• 2 comments
• 0 votes

Ah, I didn't realise that dx-spark-submit needed to be called from within the app's script. I'll give that a try.Does this work to submit a pyspark script to be run? E.g. within script.sh, I would...

• View comment
• 18 November 2022 17:23
• 0 votes

Thanks Ondrej.I can't for the life of me figure out how to get the dx-spark-submit utility though. Where is it?I've installed the dx toolkit and other commands work fine.I've tried to run it on Clo...

• View comment
• 18 November 2022 16:25
• 0 votes

How do you run a spark app?

I have read the documentation on Spark apps (https://documentation.dnanexus.com/developer/apps/developing-spark-apps), but it's not clear to me how to actually run one.   For example, I have run th...

• Former User of DNAx Community_47
• 17 November 2022 00:00
• 3 followers
• 7 comments
• 0 votes

Thank you! I would be interested to hear any comments the team has on the subject.

• View comment
• 15 November 2022 15:50
• 0 votes