I am running snippy for the E. coli sequences using one of my isolates as reference. Was able to do some but for some getting this error “ Fatal error: Exit code 2 ()”. I’d appreciate any suggestions.
Possible cause it shows: Error Type: Memory Allocation Error Severity: High
Likely Cause: The ‘samtools sort’ command is failing because the memory allocation parameter ‘-m’ is set to 0 bytes, which is below the minimum required value of 1M.
Recommended Solution:
Open the job configuration or command script where the ‘samtools sort’ command is specified.
Locate the ‘-m’ parameter in the ‘samtools sort’ command.
Set the ‘-m’ parameter to a value greater than or equal to 1M. A typical value could be 2G or 4G, depending on the available memory and the size of the data being processed.
That uses a slightly different software stack. To be clear: the memory allocated is probably not really 0 MB but should be based on the job container resources. The resources will never be less than 1 MB, which is still not enough! This is what we are investigating.
This was uncovered late last week. I’ll follow up more and link a ticket if one is needed. Thank you for reporting the issue here and our apologies for the current troubles!
