Hello!

I am encountering a similar problem using HTSeq-0.5.4p2

I tried to count reads of Arabidopsis
(TAIR10_GFF3_genes.representative.gmap.gff ) with the " -m union -s no "
options using a .sam file produced by GSNAP.

The data is paired end 101bp unstranded reads by illumina HiSeq. The .sam
files have been used previously by htseq-count to map on the same gff file
using the "-m intersection-strict" , and everything worked fine. However I
do not know which htseq-count version was used as it was done within a
Galaxy environment where I do not know the version, but most likely it
comes from 2012.
Also when I use only a short test .sam file everything works fine.


The program terminates with an error after processing a substantial number
of line pairs (for different .sam files it is a different number, probably
depends on the occurrence of a problematic read(?)):

...
4100000 sam line pairs processed.
Error occured in line 8217724 of file total1.sam.
Error: Cannot subset to zero-length interval.
[Exception type: IndexError, raised in _HTSeq.pyx:348]

I tried the same with HTSeq-0.5.4.p1 but the error was identical.


I use python2.7,  ubuntu 11.10.

I would be grateful for help

Thanks

matyas

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