Hi! I run mapping with Star for several sam files. In the end for each input file there were created these output files (which I assume is what should be): *Aligned.out.sam *Log.final.out *Log.out *Log.progress.out *SJ.out.tab
However, for one of the files the output was: *Aligned.out.sam *Log.out *Log.progress.out *STARtmp
It has been already 6 days and *STARtmp still remains. Nothing has changed. For other files the mapping was done in 1 hour. And they all have almost the same size. I wonder why *SJ.out.tab and *Log.final.out were not created for one of my files.
Could anyone tell me what can be the problem? I guess something is probably wrong with this input file...
Is it relevant that *SJ.out.tab and *Log.final.out are created in the end? I think that they are created once mapping is done... If so does it mean that the mapping is still in progress?
Do you think I can still continue with my analysis?
Have you looked through the *.Log files to see if there is a clue?
They look similar. But in *Log.progress.out of all other files is written "ALL DONE!" in the end.
Either manually inspect the last 200 lines or so to see if words "error" (etc) are present. You could try and
grepfor these/similar words to see if something obvious pops up. If for other samples mapping was done in one hour then there is no reason this sample should take 6 days.I would suggest that you start another run of that sample on the side (with new outfile names) while you investigate the logs. If it finishes fine then delete this faulty run.
Thanks a lot! I will try it then!