Hey guys,
I am trying to build a custom reference (mm9+ERCC spike-in) to reproduce some single cell RNA-seq results. I appended the mm9 genome (as a fasta file) with the ERCC sequences (also as fasta) and run the following command:
All goes well until:
Building suffix array
SACA_K called with n = 2725848238, K = 5, level 0
/usr/local/bin/gmapindex -d mm9_ERCC92 -F /stefan//scLVM//mm9_ERCC92 -D /stefan/scLVM//mm9_ERCC92 -S failed with return code 9 at /usr/local/bin/gmap_build line 375.
Any ideas what could be going on here?
I am trying to build a custom reference (mm9+ERCC spike-in) to reproduce some single cell RNA-seq results. I appended the mm9 genome (as a fasta file) with the ERCC sequences (also as fasta) and run the following command:
Code:
gmap_build -d mm9_ERCC92 mm9_ERCC92.fa -k 15 -D ~/stefan/scLVM/
Building suffix array
SACA_K called with n = 2725848238, K = 5, level 0
/usr/local/bin/gmapindex -d mm9_ERCC92 -F /stefan//scLVM//mm9_ERCC92 -D /stefan/scLVM//mm9_ERCC92 -S failed with return code 9 at /usr/local/bin/gmap_build line 375.
Any ideas what could be going on here?
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