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  • Mar 24 2016 17:46
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bmlewis-UCSD
@bmlewis-UCSD
@olgabot where is S13_kallisto/abundance.tsv
when did 13 show up ? all I have is s10
Olga Botvinnik
@olgabot
You have to run Kallisto and featurecounts on both samples
That means you still need to run Kallisto on s13
bmlewis-UCSD
@bmlewis-UCSD
where is s13?
I have no idea
Olga Botvinnik
@olgabot
In the same place as s10
TThe same folder
bmlewis-UCSD
@bmlewis-UCSD
crying face
i am looking for that now
location should be in first s10.aligh.sh file?
Olga Botvinnik
@olgabot
Yeah
Or the Kallisto sh file
I showed in class that the folder contains a bunch of files
bmlewis-UCSD
@bmlewis-UCSD
k I just changed all the s10 to s13 s in the s10.align.sh and called it s13.align.sh and ran it
i just cd there
Olga Botvinnik
@olgabot
That works! That's what I did
bmlewis-UCSD
@bmlewis-UCSD
sigh
Olga Botvinnik
@olgabot
You can do it!
bmlewis-UCSD
@bmlewis-UCSD
thanks for the help, I am gonna take a mental health break , and try some more later
LElmen
@LElmen
@olgabot Hi Olga, for importing numpy & co, I opened python (otherwise it complains about syntax), it seems it imported correctly, but then for the next step "s10_kallisto = pd.read_table('S10_kallisto/abundance.tsv', index_col='target_id')" it keeps complaining about syntax, whether I'm in bash or python. I've tried changing the ' for " etc. I also tried "load pd". Any suggestions?
[ucsd-train05@tscc-login2 processed_data]$ s10_kallisto = pd.read_table('S10_kallisto/abundance.tsv', index_col="target_id"')
-bash: syntax error near unexpected token `('
Olga Botvinnik
@olgabot
Oh that should be run IN the jupyter notebook
It's python code so bash won't like it
LElmen
@LElmen
Aha... thank you
LElmen
@LElmen

I don't understand the # "_" is the previous output

assert _.index.shape == (17,)

What am i supposed to do here?
Olga Botvinnik
@olgabot
That's the solution checking code
The_ is the previous output
Olga Botvinnik
@olgabot
You don't have to do anything with it
Youtong Huang
@smugunicorn
I accidentally deleted everything in my processed_data folder... but when I tried to resubmit things in my processing_scripts (s10_kallisto.sh, s10_sort.sh, etc), my err files keep saying "Could not open a connection to your authentication agent." I suppose this may have something to do with ssh-add we have done in the beginning but I haven't figured out what to do with this error... Would you give me a clue on what to try?
Olga Botvinnik
@olgabot
I've seen that error on tscc sometimes, I think it's their fault not yours
Which queue are you submitting to?
Youtong Huang
@smugunicorn
hotel
Olga Botvinnik
@olgabot
do you get the output files you expect?
like after s10_align.sh finishes, you get an S10.Aligned.out.sam file ?
because if you’re getting the output you expect even with this stuff in your .err files then it’s fine
Youtong Huang
@smugunicorn
I got a good Align.out file I think.
Olga Botvinnik
@olgabot
sometimes TSCC gives you a weird error in the file but your output is fine
okay is it ~30 GB ?
ls -lh to see the file size
Youtong Huang
@smugunicorn
it's exactly 30GB.
Olga Botvinnik
@olgabot
okay then you’re good!
Youtong Huang
@smugunicorn
yeah but my kallisto...
Olga Botvinnik
@olgabot
do you get the folder?
can you show the output of ls -lh ~/projects/shalek2013/processed_data ?
Youtong Huang
@smugunicorn
i get the folder, but there's nothing in it
Olga Botvinnik
@olgabot
ok what’s in the s10_kallisto.sh.err file?
Youtong Huang
@smugunicorn
hold on... I actually just deleted the folder haha.
Olga Botvinnik
@olgabot
:fire: