lobstr_index.py can't build correctly index

Open learniup opened this issue 8 years ago • 1 comments

ERROR: command 'intersectBed -a /tmp/tmpeUwvrC/lobSTR_ref_merged.bed -b /tmp/tmpeUwvrC/lobSTR_ref_plusflank_sorted.bed -wa -wb | awk '{print $1 "\t" $2 "\t" $3 "\t" $7""$8""$9";"}' | bedtools groupby -g 1,2,3 -c 4 -o concat > index_dir/lobSTR_mergedref.bed' failed.

STDOUT:

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

why always show up this problem when I build STR index, can you help me? thank you

Mar 06 '17 08:03 learniup

Hello, may I ask, did you finally get it out? How is the bed file in the --str xx.bed file generated?

Jul 28 '23 08:07 cnbdczsh