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!