Closed osilander closed 1 year ago
This is strange. The error message refers to "line 1", as if you were trying to execute a script. To help diagnose, please send the following information:
ls -l shasta-Linux-0.10.0
from the directory where you downloaded the executable.file shasta-Linux-0.10.0
from the directory where you downloaded the executable.md5sum shasta-Linux-0.10.0
from the directory where you downloaded the executable.uname -a
.I am guessing that something may have gone wrong with the curl
command you used for the download, and that you ended up with a file containing a curl
error message beginning with Not
rather than the Shasta executable. I suggest trying wget
instead, or simply downloading from a browser.
If this does not help, please send the information I requested in the previous post.
Sorry, should have checked the file contents. You're exactly right, the file was empty ("Not found"). wget also errored out. I used the download link from Chan Zuckerburg, which worked fine. Thanks for the R10 info on the other thread, I didn't look closely at the issues section and your own enhancement. I'll see how it goes with the Nanopore-May2022 model.
No problem and sorry about the confusion with the repository move. The READMEs for both the old and the new repository explain that old releases up to 0.10.0 will continue to be available from the old repository, but that is probably not sufficiently visible. GitHub does not allow me to transfer the releases to the fork. New releases will be in the fork.
The Nanopore-May2022
configuration should work with R10 reads, but will give assemblies with low contiguity and not great base level quality. Like I said, I hope to have soon (weeks) a new release with assembly configurations optimized for R10 reads.
I just realized that this problem was caused by missing information in the Getting started
page of the documentation. I fixed that and sorry about it.
Downloaded with curl, permissions changed, but simply invoking the command e.g. with './shasta-Linux-0.10.0 --help' results in this error. The more standard
./shasta-Linux-0.10.0 --config Nanopore-May2022 --input myreads.tastq
results in the same error.