Plasmer
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nekokoe
an path error
When I run Plasmer, the following error happens. I installed Plasmer by conda.
mkdir: cannot create directory ‘/intermediate’: Permission denied mkdir: cannot create directory ‘/results’: Permission denied /home/jyzhang/softwares/Plasmer/scripts/Plasmer: line 116: /intermediate/TAP_All_flye.seqkit: No such file or directory ERROR: seqkit didn't find any sequences! Please check your input file.
@Rainingfeeling Hello, I have the same issue. If you managed to solve it could you please let me know?
Hello @Rainingfeeling @Mona011 @SimranKushwaha ,
I'm sorry to hear you're encountering issues with Plasmer. To assist you better, could you please provide some additional information:
How exactly did you install Plasmer? (e.g., using Conda, from scratch, etc.) What exact command(s) are you using when you encounter this error? Understanding the specifics of your installation and the commands that lead to the error will help in diagnosing the problem and providing a more accurate solution. It’s also helpful to know whether you've attempted any troubleshooting steps on your own.
Thank you for your cooperation, and I look forward to helping you resolve these issues.
Hi, thanks for the tool.
I had the same issue (downloaded Plasmer with Conda (version:build:channel - 23.04.20:py310_1:iskoldt). From a quick look at the Plasmer code, it seemed like the "-o/--outpath" arguments were not being properly recognized, leading to attempts to mkdir at "/intermediate" and "/results" rather than at "${outpath}/intermediate" and "${outpath}/results." If you do not have sudo/root/admin privileges, you will get permission denied if you try to write files to "/"
It turns out that I used the argument "-out" instead of "-o" so I am making a note of this here in case someone else has a similar issue. I would recommend that Plasmer throw an error specifying an invalid argument in this case (if this hasn't already been accounted for). Thank you!
Hi, thanks for the tool.
I had the same issue (downloaded Plasmer with Conda (version:build:channel - 23.04.20:py310_1:iskoldt). From a quick look at the Plasmer code, it seemed like the "-o/--outpath" arguments were not being properly recognized, leading to attempts to mkdir at "/intermediate" and "/results" rather than at "${outpath}/intermediate" and "${outpath}/results." If you do not have sudo/root/admin privileges, you will get permission denied if you try to write files to "/"
It turns out that I used the argument "-out" instead of "-o" so I am making a note of this here in case someone else has a similar issue. I would recommend that Plasmer throw an error specifying an invalid argument in this case (if this hasn't already been accounted for). Thank you!
Hi @nikhilg123 , thank you for the effort! I will definitely look into it, thank you for your advice.