[lingling huang]

Not sure if this problem was solved, but I almost wonder if some of the .bax.h5 files were actually missing (not just missing in input.fofn, but that they don't actually exist). This has occasionally happened before in file transfers.

If you are still experiencing issue, try checking the input.fofn files all exist.

You can do so by downloading this simple script:

https://github.com/Magdoll/PacBio-generic/blob/master/file_exists.py

Then do
`python file_exists.py input.fofn`

If all files listed exist, it would say check passed. Otherwise it will tell you which ones are missing. Remove the missing .bax.h5 files from input.fofn.

Thank you for your reply, I've got my problem solved and produced final result.