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