Hi @mycojon
The problem with this run is the format of the data. This job will never complete and will eventually die. You can just delete then purge the output of the processing job since it is not going to be useful, and will just prevent other jobs from running.
These reads have an odd sequence identifier on the @ lines. These looks like single end reads for the first part, then these have the /1 and /2 notation at the end. Did you manipulate these yourself? Why? Maybe we can help to come up with a better analysis strategy.
What you are you trying to do here? I see that the reads came from a prior mapping job. The input to that mapping job was set as single end data but these had the odd notation on the sequence @ lines already. Do you have the original reads somewhere?
You can explain more if you want to, but I don’t think “de-interlacing” this data makes any sense, since this is not paired end data, it is single end. Getting the original reads again into Galaxy would be much better for a few reasons.
Update: Ah, mate pair data. Ok. Do you have the original reads still? What you were discussing this post? Mate-Pair Reads. Try to work with that data. The tools you are using to do the split for pairs is not going to know how to process it the way you are doing this now.
Please let me know if I can help more. 