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.

Sign up for GitHub

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

Jump to bottom

SCRAMble.R have error report. #25

Open
Ritabear opened this issue Jun 14, 2022 · 0 comments
Open

SCRAMble.R have error report. #25

Ritabear opened this issue Jun 14, 2022 · 0 comments

Comments

@Ritabear
Copy link

Hi~
I am trying to run SCRAMble.R.
I have error report by using different --ref path.
But, both of attempts can't get a success report.
1.

    Rscript --vanilla ${bin}/SCRAMble.R \
        --out-name $OUTPUT_PATH/SCRAMble_${hg}/${ID} \
        --cluster-file $OUTPUT_PATH/SCRAMble_${hg}/clusters/${ID}.clusters.txt \
        --install-dir ${bin} \
        --mei-refs ${MEI_consensus_seqs} \
        --ref /staging/biology/zxc898977/writeCodeing/debugs/ref_hg19/ucsc.hg19.blastdb.fa \
        --eval-meis \
        --eval-dels

image
2.

    Rscript --vanilla ${bin}/SCRAMble.R \
        --out-name $OUTPUT_PATH/SCRAMble_${hg}/${ID} \
        --cluster-file $OUTPUT_PATH/SCRAMble_${hg}/clusters/${ID}.clusters.txt \
        --install-dir ${bin} \
        --mei-refs ${MEI_consensus_seqs} \
        --ref /staging/biology/zxc898977/writeCodeing/debugs/ref_hg19/ucsc.hg19.blastdb \
        --eval-meis \
        --eval-dels

image

PS. ucsc.hg19.blastdb.fa is equal to ucsc.hg19.fasta
my all files structure
image

I am curious how the successful report looks like.
Hope can get a solution to produce correct reports.
Thanks a lot!
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@Ritabear