./shasta-Linux-0.10.0: line 1: Not: command not found

[osilander]

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.

[paoloshasta]

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:

• Output of ls -l shasta-Linux-0.10.0 from the directory where you downloaded the executable.
• Output of file shasta-Linux-0.10.0 from the directory where you downloaded the executable.
• Output of md5sum shasta-Linux-0.10.0 from the directory where you downloaded the executable.
• What Linux distribution are you using?
• Output of uname -a.

[paoloshasta]

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.

[osilander]

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.

[paoloshasta]

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.

[paoloshasta]

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.