buffer size exceeded with sorted bamfile
Error occured when processing SAM input (record #17287780 in file /data/DIV5/SASC/project-051-rnaveer/analysis/runs/gentrap_mcd14_sib_ls035_raw/mcd14_sib_ls035.sorted.bam):
Maximum alignment buffer size exceeded while pairing SAM alignments.
[Exception type: ValueError, raised in __init__.py:671]
This is due the fact we are using a sorted bam file, in some cases HTSeq cannot find the pair read within it's reserved buffer. The new advised practice is to us a name-sorted bam file for HTSeq.