Hello,

I am currently converting a wig file into a bigwig. This is a routine process for me. When I run:

./wigToBigWig -clip file.wig TAIR10.chrom.sizes file.bw

Here's file.wig (a snippet from the wig that was giving me trouble):

fixedStep chrom=Chr1 start=30427656 step=1 span=1
Chr1    30427656    30427657    1
Chr1    30427657    30427658    1
fixedStep chrom=Chr1 start=30427659 step=1 span=1
Chr1    30427659    30427660    1
fixedStep chrom=Chr1 start=30427662 step=1 span=1
Chr1    30427662    30427663    1
fixedStep chrom=Chr1 start=30427664 step=1 span=1
Chr1    30427664    30427665    4
fixedStep chrom=Chr1 start=30427669 step=1 span=1
Chr1    30427669    30427670    1
Chr1    30427670    30427671    7
Chr1    30427671    30427672    9
Chr1    30427672    30427673    1
fixedStep chrom=Chr1 start=30427677 step=1 span=1
Chr1    30427677    30427678    2
fixedStep chrom=Chr2 start=1005 step=1 span=1
Chr2    1005    1006    3
fixedStep chrom=Chr2 start=1008 step=1 span=1
Chr2    1008    1009    6
Chr2    1009    1010    1

I get the following result:

bedGraph error line 16 of file.wig: chromosome Chr1 has size 30427671 but item ends at 30427678

Okay, no problem, the script that made the wig probably went too far by mistake. I have encountered this before, so I use the -clip option to ignore any sites out of range:

./wigToBigWig -clip file.wig TAIR10.chrom.sizes file.bw

However, wigToBigWig then segfaults:

bedGraph error line 13 of file.wig: chromosome Chr1 has size 30427671 but item ends at 30427672
bedGraph error line 14 of file.wig: chromosome Chr1 has size 30427671 but item ends at 30427673
line 15 of file.wig: chromosome Chr1 has 30427671 bases, but item starts at 30427677
bedGraph error line 16 of file.wig: chromosome Chr1 has size 30427671 but item ends at 30427678

I have redownloaded the binary from UCSC and still get the same results. I am running on a 64-bit Red Hat server if that matters.

Has anyone encountered this before? Right now my solution is just trial-and-error editing/filtering the wigs to remove the offensive lines. I would much prefer if I could just use the -clip option as normal.

Thank you in advance!