Qiime2-2019.1 -bash: qiime: command not found


#1

hello! I just installed 2019.1 and every command I run gives me this… -bash: qiime: command not found

even when I try qiime --help , Im not sure what I did wrong, or even how to trouble shoot this.

Thank so much for the help! Appreciated!!!

Scott


(Matthew Ryan Dillon) #2

Hey there @swillyb! We see this error when you forget to activate your conda environment!


#3

hello! thank you for the reply!

the conda environment is activated, nothing seems to work

heres an example:

D25QV01EGQ17:~ Echo_Base$ source activate qiime2-2019.1

(qiime2-2019.1) D25QV01EGQ17:~ Echo_Base$ qiime --help

-bash: qiime: command not found

sorry Im not sure what I did wrong


(Matthew Ryan Dillon) #4

I wonder if something went wrong with the install… What do you see when you run conda list after activating your environment?


#5

I thought maybe that was the case, so I followed the instructions to uninstall

conda envremove -n qiime2-2019.1 conda clean -y --all

and I still have the same problem. When I run conda list it says:
EnvironmentLocationNotFound: Not a conda environment: /Users/Echo_Base/miniconda3/envs/qiime2-2019.1

clearly something has gone wrong …

Scott


#6

…I reinstalled after removing of course


#7

after removing and installing again, I have checked the envs folder for the qiim2-2019.1 folder, and its there but in it is only a conda-meta folder with nothing in it … I removed this folder and tried the install again, same result with the same folders


#8

Hello, this seems to be an issue with my computer, as I installed on another and it is ok! so thats good news,

I am however having a problem with taxa collapse, when I run this:

qiime taxa collapse
–i-table table.qza \
–i-taxonomy taxonomysilva_new2.qza
–p-level 7
–o-collapsed-table table-collapse-level-7-silva.qza

I keep getting this Error: Got unexpected extra argument ( ), right after the table line … I have no idea what this means, I can execute other commands using the table no problem.

Thanks for the help!!

Scott


(Matthew Ryan Dillon) #9

Did you forget to include \ characters at the end of the lines? It is a little hard for me to debug since it looks like maybe you didn’t copy and paste the entire error… (?)


#10

Thanks for the reply! sorry it took me bit to get back, I was out of the lab.
this is the full error, that I got again today:

(qiime2-2019.1) Behie_Comm_Prof_121318 scottbehie$ qiime taxa collapse \

> --i-table table.qza \

Usage: qiime taxa collapse [OPTIONS]

Try “qiime taxa collapse --help” for help.

Error: Got unexpected extra argument ( )

(qiime2-2019.1) airbears2-10-142-139-90:Behie_Comm_Prof_121318 scottbehie$ --i-taxonomy taxonomysilva_new2.qza \

> --p-level 7

-bash: --i-taxonomy: command not found

(qiime2-2019.1) airbears2-10-142-139-90:Behie_Comm_Prof_121318 scottbehie$ --o-collapsed-table table-silva-7.qza

-bash: --o-collapsed-table: command not found

(qiime2-2019.1) Behie_Comm_Prof_121318 scottbehie$

thanks for the help here, I really appreciate it!!!

Scott


(Matthew Ryan Dillon) #11

Perfect, thanks @swillyb!

These are both indicators that you might not have included the \ character at the end of your lines to signify a line break (see my question/comment above). Please see this post for a summary of this topic: Qiime deblur denoise-16S


#12

I made sure to have the backslashes in, this is exactly what Ive been entering. No doubt Im doing something wring, I just don’t know what it is.

qiime taxa collapse
–i-table table.qza \
–i-taxonomy taxonomysilva_new2.qza
–p-level 7
–o-collapsed-table table-silva-7.qza

thanks for the help!

Scott


(Matthew Ryan Dillon) #13

I still only see one backslash in your command. You either need to escape each line break (opt 1) or put all of the command on the same line (opt 2):

# option 1
qiime taxa collapse \
  --i-table table.qza \
  --i-taxonomy taxonomysilva_new2.qza \
  --p-level 7 \
  --o-collapsed-table table-silva-7.qza
# option 2
qiime taxa collapse --i-table table.qza --i-taxonomy taxonomysilva_new2.qza --p-level 7 --o-collapsed-table table-silva-7.qza

#14

ok great! I promise they have the slashes, something went weird with the copy paste, however option 2 works! … i do copy paste commands so something must be odd with that… I don’t know! thank you so much!!!

Scott