seqGSEA / HTSeq problem

[dietmar13]

using seqGSEA package I have some problems. I have already used it with success, but now I get this error:

Traceback (most recent call last):
  File "/home/ws/SW_install/SeqGSEA/count_in_exons.py", line 146, in <module>
    for af, ar in HTSeq.pair_SAM_alignments( tmp_obj ):
  File "/usr/lib64/python2.6/site-packages/HTSeq-0.5.4p2-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 621, in pair_SAM_alignments
    for p in process_list( almnt_list ):
  File "/usr/lib64/python2.6/site-packages/HTSeq-0.5.4p2-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 605, in process_list
    assert a1.pe_which == "second"
AssertionError

My SAM/BAM files were produced with RUM and are name-sorted.
the flattened gtf looks good (and as said above, was already used with success).

Perhaps I have updated the HTseq python package after successful usage, but I don't know it for shure.

Do someone have any clue what could be wrong?

best wishes,

dietmar