I hope this finds everyone having a great summer! I am running Qiime2 (currently 2019.4) on Linux for microbiome data analysis. Last week, I started having issues running codes. Some of my codes would not fully paste into summit, resulting in an error output, then it would paste the rest of the cod…

One down, one to go! :wink: May be an OS issue. The small print on the click documentation page you found (good sleuthing, btw! :male_detective:) suggests some alternative formats for the export command you tried. Details here: [image] RuntimeError: Click will abort further execut…

Hey Scott! Welcome to the forum. Your post is pretty broad - if it's ok by you, I'd like to start small. :microbe: Based on the command you screencaptured, and the error message it produced, it looks like you might not be passing all of the required arguments to the qiime demux emp-paired command. …

@WrigleyS try to nano the code into a bash file and then submit it to slurm. It looks like from the input your placed on the command prompt the code executed before you submitted all of your commands (as Keefe pointed out). Writing shell scripts - Lesson 1: Writing your first script and g…

Chris, I appreciate the reply! No worries on starting broad. I totally understand. I had everything in the code, including what was in red. "(1/1) Missing Option --o-error-correction-details"....The problem is, when I copy and paste the code from my text editor, it doesn't all paste initially. Th…

Ben, Thank you for the reply! I will give this a try. I normally nano and sbatch to .txt files. I'll try .sh to see if that makes any difference!

by the way, it may not be recognizing the "" to tell it to go to the next line. Could this be because of some text issue? Copy/paste it into a text editor and then paste it into the command line? Ben

Ben, Thanks for the script suggestion. I ran it as follows with the following input, however I still get the same slurm error message that is also below. nano beet-saliva.sh chmod a+xwr beet-saliva.sh sbatch beet-saliva.sh With the following script: #!/bin/sh #SBATCH --job-name=demux_beet_sali…

@WrigleyS , if you read your command closely, you'll notice a \ character missing at the end of your second-to-last line. [image] ChrisKeefe: The \ characters are escape characters that let you write one command on multiple lines. Without that character, you are telling the command line to ru…

Chris, Thank you again for your assistance! I really appreciate it! I did correct that missing bit of code (), however, I still get the same exact error with my sbatch about the ASCII as encoding for the environment and the locales as I was before. :frowning: #!/bin/sh #SBATCH --job-name=demux_b…

Chris, Thank you so much for all your help! I've been at this 5 months so this is still pretty fresh to me. Once the command line issue was corrected, I utilized LC_ALL=en_US.UTF8 and my code ran. I don't want to take up all your time, but I have one more question. Will I have to run the above lo…

Great question, @WrigleyS ! I've never had this issue myself, so your best bet is probably to try it and find out. :face_with_monocle: If I had to guess, it will probably stick through the whole session. If you get tired of setting this variable at login, you could probably add your locale-setting c…

Issue Running Codes

Technical Support

ChrisKeefe (Chris Keefe) June 12, 2019, 10:28pm 11

One down, one to go!
May be an OS issue. The small print on the click documentation page you found (good sleuthing, btw! ) suggests some alternative formats for the export command you tried. Details here: