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Core NGS Intro class zoom - Shared screen with speaker view
Melanie A. Murphy
01:23:23
How does this work if we are using Putty?
Dennis Mishler
01:23:32
can you repaste the text here?
Melanie A. Murphy
01:24:32
Yes, can you please paste here? I am having trouble seeing it in the command window.
James Dong
01:24:35
for some reason there is an error
Anna Battenhouse
01:24:40
ssh abattenh@login5.ls5.tacc.utexas.edu
Dennis Mishler
01:24:40
mine says access denied... hmmm
Vy Dang
01:25:09
Ssh yourusername@login5.ls5.tacc.utexas.edu
Vy Dang
01:25:12
for terminal
Vy Dang
01:25:30
Its auto uppercase for me
James Dong
01:31:11
wait for some reason I cant even login to ls5.tacc.utexas.edu now on putty
James Dong
01:31:17
it says the host does not exist
Vy Dang
01:32:30
Did you change the setting in putty back to ls5.tacc….
Riddhiman Garge
01:32:50
@James- could you share the ssh command you typed into the command line?
James Dong
01:33:17
i tried connecting to host name ls5.tacc.utexas.edu
James Dong
01:33:34
I've done this before I don't know why its not working now
Vy Dang
01:34:05
I’ll ask Anna to put you and one of us in a breakout room
Riddhiman Garge
01:36:39
@James I don’t see you in the breakout room.
James Dong
01:38:23
ok I just had to restart my computer it all works now
Vy Dang
01:39:47
Hey James, next time if you don’t come in to a breakout room, please let us know because the person in the waiting room didn’t know what was going on :)
James Dong
01:46:06
yes I will next time sorry. I think my computer's network was messed up because when I tried joining the breakout room, there was also an error.
Md Hassan Uz Zaman
01:48:33
Is the percentage thing (when you use less or more) general for these commands? Or is this a special feature of this login node we're using?
Md Hassan Uz Zaman
01:48:55
(by percentage thing I meant how the commands show how much of the file you're through)
Riddhiman Garge
01:50:56
@Hassan, yes the % shows how much of the file you’ve read.
Riddhiman Garge
01:51:31
I believe it is a general feature too.
Md Hassan Uz Zaman
01:51:52
thanks!
Md Hassan Uz Zaman
02:00:39
1/4th
Denise Furr
02:34:42
break?
Simon Lee
02:38:12
should I load unzip? I have error message "command-not-found"
Vy Dang
02:38:51
try gunzip
Vy Dang
02:38:54
See if it works
Simon Lee
02:39:12
nvm. typo
Dennis Mishler
03:22:00
I can't seem to get that log file to display
Dennis Mishler
03:22:27
Keep getting "no such file or directory: 'miRNA_test.fq"
Vy Dang
03:24:52
Could you send what your command was @Dennis?
Dennis Mishler
03:25:46
more miRNA_test.cuta.log
Dennis Mishler
03:26:10
then says "cutadapt version 1.14..." and goes for a while
Dennis Mishler
03:26:26
finishing with "No such file or directory: 'miRNA_test.fq"
Vy Dang
03:27:05
The .log file documents the process of the script/command you were running
Vy Dang
03:27:24
That means you didnt have the 'miRNA_test.fq" file and that’s the error
Dennis Mishler
03:27:39
hmmm... okay, must have missed something
Nandini Aiyappan
03:27:55
-bash: /work/projects/BioITeam/common/script/trim_adapters.sh: Permission denied
Nandini Aiyappan
03:28:23
Its saying permission denied for for the shell script on the BioITeam
Nandini Aiyappan
03:28:42
In my error log file
Vy Dang
03:29:11
What are you trying to do? Are you trying to edit the file?
Nandini Aiyappan
03:29:32
No - just when I submit the job to the queue
Dennis Mishler
03:34:12
do we need to recopy/make, or just run?
Dennis Mishler
03:42:32
How much more new content for today?
Claudia Jou
03:53:38
it did not honor the reservation yesterday in Dhivya's class
Claudia Jou
03:57:23
we had to run the jobs without the reservation for them to work!
Claudia Jou
03:57:55
blocked
Albert MacKrell
04:04:31
How do I know if the job I submitted worked? I feel like I have no idea what output files to look at and how to evaluate them.
Riddhiman Garge
04:07:02
@Albert you should be good if the log file was fully populated without errors I believe.
Eric Young
04:11:26
Thank you everyone! :) :)
Luciano Cantu
04:11:38
thank you, see you tomorrow