This is probably really simple but im stuck trying to reverse transcribe i copied the code from above in the tutorial:
qiime rescript reverse-transcribe
however i keep getting :
There was a problem with the command:
(1/1) Missing option '--o-dna-sequences'. ("--output-dir" may also be used)
--o-dna-sequences: command not found
Given that i used the code from above i cant work out why this wont run?
Open to suggestions TIA
Hi @SimonD, welcome to !
It is hard to tell from your post, but I assume you have
\ at the end of each line, except for the last, when running in the terminal?
If so, are these commands being typed into the terminal directly, or being copied and pasted? Sometimes, when copying commands, hidden characters make it into the command. Then when you paste them into the terminal, the terminal interprets these hidden characters as "end of input" and tries to execute the partial command.
One sanity check is to try again by typing in the command manually on one line like so:
qiime rescript reverse-transcribe --i-rna-sequences silva-138.1-ssu-nr99-rna-seqs.qza --o-dna-sequences silva-138.1-ssu-nr99-seqs.qza
You can also, try restarting your terminal and environment, and retry the command. If the issue still persists, let us know. I am sure others on the forum may have additional advise.
Thanks, feeling a bit of a plonker now! I typed into the terminal this time, I've got lazy using copy and paste to move code to the terminal rather than typing out my commands like i used to and i'm guessing that was the problem. Lesson one of Bash, check your code!!