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LElmen
@LElmen

!/bin/bash

PBS -q hotel

PBS -V

PBS -N s13_kallisto

PBS -e s13_kallisto.sh.err

PBS -o s13_kallisto.sh.out

PBS -l nodes=1:ppn=8

PBS -l walltime=0:30:00

kallisto quant --index /projects/ps-yeolab/biom262-2016/genomes/mm10/gencode/m8/gencode.vM8.pc_transcripts.kallisto$
--threads 8 --output-dir $HOME/projects/shalek2013/processed_data/S10_kallisto \
$HOME/projects/shalek2013/raw_data/S13_R1.fastq.gz \
$HOME/projects/shalek2013/raw_data/S13_R2.fastq.gz
Olga Botvinnik
@olgabot
yeah that dollar sign shouldn’t be there
that’s where the “\” should o
go
it’s hard for me to read this
can you format it with three backticks “```” on an otherwise empty line at the beginning and end of the message?
LElmen
@LElmen
Screen Shot 2016-02-12 at 3.13.06 PM.png
Olga Botvinnik
@olgabot
oh hmm that may be a formatting thing
Can you add a backslash after —index and press ENTER ?
the index file is very long and it’s hard to tell waht’s going on
(make sure there’s no spaces or tabs after —index)
oops I mean after the “\” (backslash)
LElmen
@LElmen
Screen Shot 2016-02-12 at 3.15.00 PM.png
The $ disappeared when I did that
Olga Botvinnik
@olgabot
okay yeah nano was using the $ to show the line still continues
that’s what I suspected
LElmen
@LElmen
aha
Olga Botvinnik
@olgabot
hmm I say double-check for spaces after the backslashes and run again
it might have been a heisenbug
LElmen
@LElmen
heisenbug?
Olga Botvinnik
@olgabot
(a bug that you see once and never see again)
LElmen
@LElmen
oh weird
Olga Botvinnik
@olgabot
or you can observe but can’t pinpoint the reason
LElmen
@LElmen
I'll try to run it again
Olga Botvinnik
@olgabot
ok great
LElmen
@LElmen
This isn't working. For s13 I got the long error message again, then I tried to re-run s10 naming the job s10again and it didn't create any output either, but the error was different.
Screen Shot 2016-02-12 at 3.39.50 PM.png
Olga Botvinnik
@olgabot
yay different error!
my favorite!
hmm does the folder ~/projects/shalek2013/processed_data exist?
did you make the soft link from scratch?
LElmen
@LElmen
yes, ls
Olga Botvinnik
@olgabot
can you show ls -lha ~/projects/shalek2013/
LElmen
@LElmen
Screen Shot 2016-02-12 at 3.42.52 PM.png
Olga Botvinnik
@olgabot
okay perfect
now can you show ls -lha ~/projects/shalek2013/processed_data
there’s something weird going on with permissions
LElmen
@LElmen
Screen Shot 2016-02-12 at 3.43.57 PM.png
Olga Botvinnik
@olgabot
oh right you have to cd first
cd ~/projects/shalek2013/processed_data
ls -lha
soft links are funny like that
LElmen
@LElmen
Screen Shot 2016-02-12 at 3.46.21 PM.png
Olga Botvinnik
@olgabot
wait someone else has been there
bmreilly
LElmen
@LElmen
I have an S10_kallisto folder from when we did this in class, but I'm not sure it is right. I can't do the S10_kallisto.shape
Olga Botvinnik
@olgabot
and they’ve made it so you can’t edit anything
LElmen
@LElmen
?
Olga Botvinnik
@olgabot
check out the permissions: -rw-r—r—
the first - means not a folder
then the first trio of rw- is for the user, who is bmreilly and can read-write-execute