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  • Mar 24 2016 17:46
    bmlewis-UCSD synchronize #107
  • Mar 15 2016 23:44
    apryan opened #130
  • Mar 15 2016 10:59
    anupriyatripathi opened #129
  • Mar 13 2016 21:14
    andersonbrookee synchronize #76
  • Mar 13 2016 21:12
    andersonbrookee synchronize #76
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    bioh4x on master

    Update index.jade (compare)

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    Update index.jade (compare)

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    adding new last lecture powerpo… (compare)

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  • Mar 08 2016 03:01

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    week10_mod1_updates (compare)

  • Mar 07 2016 00:05
    ohsamboss opened #128
  • Mar 04 2016 22:24

    olgabot on gh-pages

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  • Mar 03 2016 15:44

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Olga Botvinnik
@olgabot
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:
Youtong Huang
@smugunicorn
Screen Shot 2016-02-12 at 9.34.44 AM.png
Olga Botvinnik
@olgabot
okay see where it says “file not found"
Youtong Huang
@smugunicorn
yeah
Olga Botvinnik
@olgabot
that’s because in the script it says [S10 R1 fastq file] and [S10 R2 fastq file] which indicates that you need to replace that placeholder with the real file
the file names are in the s10_align.sh file
Youtong Huang
@smugunicorn
um... oh... wait LOL i got confused and just copy pasted your codes
Olga Botvinnik
@olgabot
side note - I’m surprised the username @smugunicorn has not been taken until now!
yeah you gotta read them!
Youtong Huang
@smugunicorn
hahah xD
Olga Botvinnik
@olgabot
remember: “copy-paste-think"
Youtong Huang
@smugunicorn
T^T yessss it worked... thanks so much @olgabot
Olga Botvinnik
@olgabot
yayy!!!!!!
“copy-paste-think” is a lot of programming/bioinformatics .. someone out there has a solution to something that’s slightly different so you have to think about what you need to change for yours
is the video call for today
so you can type git co[TAB] and it’ll autocomplete git commit
mbaughn
@mbaughn
Thank you!
LElmen
@LElmen
I can't find the instructions for how to I kill a specific job on tscc? I forgot to rename the jobs and some other details so I had to resubmit, but now I have several jobs running. I thought ctrlC killed all jobs, but they are still running?
ecwheele
@ecwheele
qdel jonid#
jobid#
LElmen
@LElmen
Thank you!
LElmen
@LElmen
ls
Olga Botvinnik
@olgabot
?
I can tell you what files I currently have
Alannah Miranda
@ahmirand
my s10_featurecounts.txt file has an extra column that is headed by the code i used to run the featurecounts job... and every time i get rid of said column the next few cells don't work/have an assertion error and when i leave the column in, i think the cells are still returning wrong answers. I've tried rerunning the job and compared it with the code that is in the notebook we worked on in class, but i can't figure out whats wrong. halp pls :disappointed_relieved:
Olga Botvinnik
@olgabot
can you show the code?
we can fix this
Alannah Miranda
@ahmirand
Screen Shot 2016-02-12 at 12.55.45 PM.png
here's the code from the notebook, but did you want to see what I used for to run the job too?
Olga Botvinnik
@olgabot
yeah that looks correct