Troubleshooting

This section contains random issues that have arisen, so something here may be helpful.

Rename files that have a special character

This command rename files that have a special character to remove special character. Special characters (+/!@#$%^ etc) can cause problems in file names as many programs will not recognize them. Uses Linux "rename" not perl.

rename SPECIALCHAR _ *.fq

Example:

rename + _ *.fq

No assembly-reads in folder

This happens usually at the remove duplicates or paired-end read merging step because of insufficient memory. Some samples might need more memory because of: high or low sequencing depth, degradation in the sample, or a whole lot of data. I have found that I need up to 100 gb of memory to process these difficult samples.