Paired end reads don't have the same length

[Vio]

Hi,

My genomes were sequenced by illumina paired end. I was running cortex but it died in SAM line1 says the list of paired end reads don't have the same length and quit.

"These lists of paired end files are not the same length at /CORTEX_release_v1.0.5.21/scripts/calling/run_calls.pl line 1959, <SAM> line 1."
 
I processed my files, but i lost to 25% of my info.

[Zamin Iqbal]

What do you mean lost 25% of your info. I think most likely the reason it thinks the LISTs of fastq are of different lenght is that one has a carriage-return at the end of the last line and another does not

Z