Bowtie 2.0 takes too long to complete

Bowtie2.0 task is running for a long time. It has been 36 hours and still running. Is that normal? Thanks! I am analyzing ATAC-seq data with paired end reads.

It is giving me the following stats although it is still running. Can someone please tell me why? thanks

Hi @abhay03

It looks like the job is still completing the process of writing all the output files. Let this complete to avoid needing to rerun.

If you were working at, I can let you know that the clusters were very busy when you wrote in, and are a bit less busy now.

Yes, sometimes, since those 3 days probably included queue + the actual job execution time. The best advice is to get jobs queued then let them complete. Using collections and workflows will significantly improve total processing time.

If you think there is still a problem after a few more hours, please either reply and post back a share link to the history and note the dataset involved, or ask for a moderator to start up a direct chat to post that in privately.