Hi,
I am trying to map one assembly of Verticillium Longisporum to another
one, based on the description at
http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt
When I try to carry out the step
chainMergeSort chainRaw/*.chain | chainSplit chain stdin,
which is
chainMergeSort au13_au16.chain > au13_au16_sorted.chain
chainSplit chain au13_au16_sorted.chain
in my case, I get the error message
sh: Pipe call failed
command exited with 2: cat chain/meta.tmp | sort -u >
chain/scaffold458.chain
regarding the execution of chainSplit. Since it takes chainSplit a few
seconds to crash, I assume the error is not trivial (like taking the
wrong input file).
Does anyone have an idea what causes this error and how to fix it (I
have attached au13_au16_sorted.chain in compressed form)?
Thanks
Ingo
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