Zoom Logo

Core NGS Intro class zoom - Shared screen with speaker view
Eduardo Castro
01:48:23
logged on
Melanie A. Murphy
01:48:32
got it and been following along.
Amina Zeidan
01:51:26
Permission denied, cannot create directory
Amina Zeidan
01:51:45
Yes I did
Denise Furr
01:52:30
I was in the wrong directory and put it in scratch instead.
Md Hassan Uz Zaman
01:54:31
"wget: missing URL"
Riddhiman Garge
01:56:29
@Hassan try it again. Sometimes the link might have not pasted properly
Md Hassan Uz Zaman
01:57:52
Can I be put in a breakout room with you @Riddhiman?
Md Hassan Uz Zaman
01:58:02
to solve this
Melanie A. Murphy
01:58:38
Is it possible to set up the command window so it does not get covered by the wiki page as you go back and forth?
Melanie A. Murphy
02:00:37
I am getting " mkdir -p $STRATCH/data/test1mkdir: cannot create directory '/data': Permission denied"
Melanie A. Murphy
02:00:57
Oh, shoot!
Dennis Mishler
02:06:39
I remember cd .. from the 80s!
Dennis Mishler
02:08:27
does "recursive" mean all files within the directory?
Md Hassan Uz Zaman
02:17:32
this sounds like -w just converts rsync to cp (except not exclusively local)?
Nandini Aiyappan
02:24:56
It works for me on a Mac too
Dennis Mishler
02:32:43
Should "cat" with CORENGS work for me (as it did with you)?
Lydia Tressel
02:34:38
does anyone know what the password is?
Md Hassan Uz Zaman
02:34:56
SequencingDataIsK00l!
Lydia Tressel
02:35:04
Thanks :)
Chloe Atallah
02:35:16
I'm only in this group, it says G-816696
Chloe Atallah
02:36:11
yup 07456 catallah
Denise Furr
02:36:27
Mine says authentication failed.
Kiley Evans
02:36:48
Mine does too^
Chloe Atallah
02:37:21
thank you!
Lydia Tressel
02:37:30
Are you sure that is the password?
Md Hassan Uz Zaman
02:37:42
It worked for me...
Albert MacKrell
02:37:57
Unix file permissions: with great power comes great responsibility
Lydia Tressel
02:37:58
is it K-0-0-l
Nandini Aiyappan
02:38:07
K00L!
Nandini Aiyappan
02:38:20
Sorry-small case l
Nandini Aiyappan
02:38:33
And its zeros not O
Riddhiman Garge
02:38:40
@Kiley @ Denise I’d retype the password instead of copying.
James Dong
02:39:29
It said that the authenticity of the host cant be established
Kiley Evans
02:39:38
It worked now!
Albert MacKrell
02:40:09
say "yes" James
Denise Furr
02:40:20
This is going too fast for me.
James Dong
02:40:40
I typed yes and it says authentication failed. it doesn't prompt me for a password
Vy Dang
02:41:20
what is your full scp command James?
Shuge Sun
02:41:33
After I typed the password, I got permission denied
Dennis Mishler
02:41:41
Anna, were we supposed to copy 1 file or many files?
Lydia Tressel
02:42:53
It worked when I copied and pasted the password XD
Shuge Sun
02:43:09
Can someone send the password again? thax
Shuge Sun
02:43:11
thx
Anna Battenhouse
02:43:26
SequencingDataIsK00l!
Anna Battenhouse
02:43:39
00 + lowercase l (not 1)
Shuge Sun
02:44:20
Still saying “authentication failed”
Shuge Sun
02:45:41
Ok it’s good now
Simon Lee
03:24:56
Just added to that, Sequencing companies are developing Unique Molecular Identifiers that is added before PCR so they can distinguish the duplicate from PCR or biological
Simon Lee
03:25:17
fyi
Claudia Garcia Jou
03:50:05
typing bwa by itself works for me!
Amina Zeidan
03:50:18
Yes, it worked for me too
Dennis Mishler
03:50:19
bwa worked for me, fyi
Albert MacKrell
03:51:24
worked for me too
Albert MacKrell
03:51:44
hostname
Dennis Mishler
03:52:34
can you list modules?
Vy Dang
03:52:56
Module avail
Vy Dang
03:53:06
that will give you all modules
Vy Dang
03:53:20
Or you can list your own module too @dennis
Dennis Mishler
03:53:32
there are a lot
Vy Dang
03:54:04
Do you just want to see what you are having?
Dennis Mishler
03:55:49
curious to know what is loaded/not loaded
Vy Dang
03:56:03
Then you can do: module list
Dennis Mishler
03:56:27
great
Denise Furr
04:05:11
my biocontainers didn't load properly
Vy Dang
04:05:20
whats the error?
Denise Furr
04:05:46
I don't have the list and the programs don't load with module
Vy Dang
04:06:27
What happens when you type ‘module load biocontainers’
Denise Furr
04:07:10
I get a lot of messages about biocontainers
Vy Dang
04:07:24
Could you please copy the first couple lines?
Denise Furr
04:08:09
I don't know how to copy the lines
Dennis Mishler
04:19:53
anna, my queue started at 11:58:55, still waiting
James Dong
04:21:26
for some reason it says my launcher creator.py command not found
Vy Dang
04:21:42
@James did you load launcher
Albert MacKrell
04:22:33
launcher_creator is on my path but is not running
Albert MacKrell
04:22:49
yes
Albert MacKrell
04:22:52
didt
James Dong
04:23:04
i think my laucher_creator.py is on my home
Albert MacKrell
04:23:10
launcher_creator.py -j simple.cmds simple -t 00:00:05 -w 8 -q development
Dennis Mishler
04:23:21
Anna, tacc queue looks really long
Dennis Mishler
04:23:31
like tons of requests just today
Albert MacKrell
04:24:47
Sorry late for a meeting. I will have to sort tomorrow
Vy Dang
04:24:59
then you can run it from your home dir @James
James Dong
04:28:39
I don't think its working
Vy Dang
04:29:51
we can look into it after Anna finishes lecturing this @James
Nandini Aiyappan
04:31:57
Sorry I have to leave. Will catch up with the video later on. Thanks
Simon Lee
04:32:41
I need to go. will catch up with video. Thx. See you tomorrow