Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

lobstr_index.py can't build correctly index #80

Open
learniup opened this issue Mar 6, 2017 · 1 comment
Open

lobstr_index.py can't build correctly index #80

learniup opened this issue Mar 6, 2017 · 1 comment

Comments

@learniup
Copy link

learniup commented Mar 6, 2017

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

@cnbdczsh
Copy link

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants