I'm following pbalign tutorial on large datasets. I split my original fofn into subsets containing only three bax.h5 files, there is 14 of them.

I run pbalign as following:

pbalign file_1 reference.fasta out_file_1.cmp.h5 --forQuiver

For every single subset of original fofn I get error message:

[ERROR] SortService returned a non-zero exit status.

Unfortunately there is no more informative messages.

Additionally for one subfile I get different message instead:

[ERROR] FilterService returned a non-zero exit status. Error parsing alignment line 103. Missing or error in field PNEXT

The original movies are about ~1GB in size.

I'm using pbalign as part of smrtanalysis_v2.3.

I went ahead and tested the same approach on just a subset of a movie with:

pbalign -vv file_1.bax.h5 reference.fasta out_file_1.cmp.h5 --forQuiver --algorithmOptions=' -holeNumbers 1-5000 ' --keepTmpFiles

but still got the same error message:

[INFO] pbalign version: 0.2.0.138342
...
[INFO] ForQuiverService: Sort.
[INFO] SortService: Sort a cmp.h5 file using cmph5tools.py.
[DEBUG] SortService: Call "cmph5tools.py -vv sort --deep --inPlace out_file_1.cmp.h5 "
[ERROR] SortService returned a non-zero exit status.

No other messages returned. sam file gets created. Seems to be formatted the right way. Any piece of advice would be appreciated.