TSS plot with htseq 0.6.1 gives segmentation fault

I am trying to run htseq with a bam and gtf file to create a TSS plot. After a while got a segmentation fault (core dumped). Im running the code shown in the example. I tired running it on a smaller file and this gave me no error...

bamfile = HTSeq.BAM_Reader( "s_8_1_I12-1251-03_DP-H3K27Ac.chipseq.hg19.srt.bam" )
gtffile = HTSeq.GFF_Reader( "hg19_IlluminaAnnotation_genes.gtf" )
coverage = HTSeq.GenomicArray( "auto", stranded=False, typecode="i" )

for almnt in bamfile:
    if almnt.aligned:
        coverage[ almnt.iv ] += 1

tsspos = set()
for feature in gtffile:
    if feature.type == "start_codon" and feature.:
        tsspos.add( feature.iv.start_d_as_pos )

p = HTSeq.GenomicPosition( "1", 145439814, "+" )

print p in tsspos

halfwinwidth = 3000
window = HTSeq.GenomicInterval( p.chrom, p.pos - halfwinwidth, p.pos + halfwinwidth, "." )

list( coverage[window] )  
wincvg = numpy.fromiter( coverage[window], dtype='i', count=2*halfwinwidth )
print wincvg

pyplot.plot( wincvg )
pyplot.show()

I have no idea what is error means. It is a memory problem? or is there might be something wrong with the file?

tss-plot python chip-seq htseq

• 3,078 views • link

updated 4.9 years ago by Ram

• written 12.3 years ago by jellevandewege

Did it create a core dump when it crashed? Also, is it possible that you ran out of memory (unlikely, but it's possible). Finally, are you able to run the full version line by line to determine at what point it breaks?

• 0 views • link

written 12.3 years ago by Devon Ryan