I have been trying to run sff_extract using the -l flag to
extract the paired end read from my sff file but I receive
the following error.
brian@Gaff[Pairedend_extract] sff_extract -o testrun -l
/home/brian/Neo_home/test/Pairedend_extract/LINKER/Linker.fasta
/home/brian/Neo_home/test/FE4758201.sff
[ 1:21PM]
Working on '/home/brian/Neo_home/test/FE4758201.sff':
Creating temporary sequences from reads in
'/home/brian/Neo_home/test/FE4758201.sff' ... done.
Searching linker sequences with SSAHA2 (this may take a
while) ... Input parameter error for "-solexa"
An error occured during the SSAHA2 execution, aborting.
I am unsure what exactly is causing the error as SSAHA2
works fine outside of sff_extract and sff_extract works perfectly
when not using the -l flag
regards
Brian
extract the paired end read from my sff file but I receive
the following error.
brian@Gaff[Pairedend_extract] sff_extract -o testrun -l
/home/brian/Neo_home/test/Pairedend_extract/LINKER/Linker.fasta
/home/brian/Neo_home/test/FE4758201.sff
[ 1:21PM]
Working on '/home/brian/Neo_home/test/FE4758201.sff':
Creating temporary sequences from reads in
'/home/brian/Neo_home/test/FE4758201.sff' ... done.
Searching linker sequences with SSAHA2 (this may take a
while) ... Input parameter error for "-solexa"
An error occured during the SSAHA2 execution, aborting.
I am unsure what exactly is causing the error as SSAHA2
works fine outside of sff_extract and sff_extract works perfectly
when not using the -l flag
regards
Brian
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