OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21.
Nobody has claimed this yet.
- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
- No merged PRs in 30d
Description
I tried to run smartpca.pl for this par file and every input files are in the same directory from where I tried to run smartpca.pl. However, I get error every time saying OOPS -i flag not specified at /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21.
My Par file looks like
genotypename: p1_nor_non_nor_sicca_merged.bed
snpname: p1_nor_non_nor_sicca_merged.bim
indivname: p1_nor_non_nor_sicca_merged.fam
evecoutname: p1_nor_non_nor_sicca_merged.pca.evec
evaloutname: p1_nor_non_nor_sicca_merged.eval
altnormstyle: NO
numoutevec: 10
numoutlieriter: 5
numoutlierevec: 10
outliersigmathresh: 6
qtmode: NO
familynames: NO
Please some one could help me. I will appreciate any help
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by comparing the reported smartpca.pl invocation with the error from /usr/local/analysis/eigensoft/5.0.1/bin/smartpca.perl line 21. Check how the supplied par file and its genotypename, snpname, and indivname entries are passed to the tool. Done means identifying the missing -i argument or documenting the required invocation and confirming it with the provided parameter file.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- perl
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100