scatter_count > 50

[RoniHaas]

Hey @yashpatel6 ,
I think I am having memory problems:

Process `multi_sample_wgs:calculate_contamination_tumour:run_GetPileupSummaries_GATK (1)` terminated with an error exit status (247)

How much would you recommend increasing the scatter_count?

[yashpatel6]

The contamination calculation processes run on the merged BAM so increasing the scatter count won't have any effect. Could you point me to the log file for the job that failed?

[RoniHaas]

Sure, Thanks for the help!

In this directory the csv, config and log files are found:
/hot/users/rhaas/Input/case_study/gSNP/(*config|*csv|*log)

I used the previous release (it was before you sent the email)

[yashpatel6]

Got it, thanks!

The release shouldn't affect this part of the pipeline, I'll run some tests and check the problem.

[yashpatel6]

I tried some test runs and, you're right, it does seem like a memory error. Resolving it would require the memory allocation for that process in the pipeline to be increased.

[RoniHaas]

I tried some test runs and, you're right, it does seem like a memory error. Resolving it would require the memory allocation for that process in the pipeline to be increased.

Thanks for the update! No problem, I will re-run once the changes in memory allocation are committed.