utritala

Hi Robert, Thanks for your prompt response. The contig names don't have any white spaces. For example: ``` >contig_1 >contig_10 >contig_100 >contig_10001 >contig_10002 >contig_10005 >contig_10007 >contig_10009 >contig_1001 >contig_10011 ``` Can...

Sure. I can share a subset of it shortly.

OK. I have tested the same command with a subset of the data (100 contigs, 100000 reads for polishing) and interestingly it doesn't produce this error anymore. The original data...

Thanks Robert. OK will do.

Hi Robert, I have emailed you the links to some sample files as well as contig headers. Thanks, Urmi

No worries Robert. Thanks you so much for looking into it. On Mon, Jul 8, 2019 at 9:22 AM Robert Vaser wrote: > Thanks Urmi, I am currently looking at...

Good point about the short contigs. It took about 45 minutes to reach the error. I used minimap2 to generate the SAM file.

OK I can try that. I will let you know how I get on. Thanks again for your help.

Running the full dataset with PAF files worked like a charm. Thank you so much once again, Robert. :)