Dear Galaxy Biostar team,
I'm seem to be having a problem running Samtools SAM-to-BAM conversion on two BWA mapped paired end SAM files that have been associated with a custom reference genome so I can run SNP analysis with the GATK. The file size for the SAM files are from 10-20Gb in size and the genome file is 2.7Gb, may this be an issue? When I run the SAM-to-BAM tool using the custom reference genome located in the history on the aforementioned files I receive the following error after executing the process:
This has occurred in the last few days and I'm slightly worried I've done something wrong in the processing of my data. Any help with this problem would be greatly appreciated.