sh: smartpca: command not found
Nobody has claimed this yet.
- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
- No merged PRs in 30d
Description
Hello,
I downloaded in the current directory from where I am running smartpca.perl that script and evec2pca-ped.perl
I was running:
perl smartpca.perl -i output5F.bed -a output5F.pedsnp -b output5F.pedind -o output5F.pca -p output5F.plot -e output5F.eval -l output5F.smart
pca.log -m 5 -k 3 -t 2
smartpca -p output5F.pca.par >output5F.smartpca.log
sh: smartpca: command not found
OOPS couldn't open file output5F.pca.evec for reading at smartpca.perl line 65.
Can you please tell me how to resolve this?
I made both scripts executable via:
chmod a+x evec2pca-ped.perl
chmod a+x smartpca.perl
Please advise,
Thanks
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 with smartpca.perl and the reported command sequence, checking how the smartpca executable is expected to be located when the script runs. Reproduce the command using output5F.pca.par and verify that smartpca runs and produces output5F.pca.evec instead of the reported missing-file error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c, perl, shell
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100