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Alannah Miranda
@ahmirand

and when I use this to remove the last column:

s10_featurecounts = pd.read_table('s10_featureCounts.txt', skiprows=1, index_col=0, usecols= ['Chr', 'Start', 'End', 'Strand', 'Length'])

I get this error:

Olga Botvinnik
@olgabot
why doesn’t it look right to you>
and whih column are you removing?
remember that the example data is usign ucsd-train01
so every time you see ucsd-train01 you need to replace that with ucsd-train17
You NEED that big column because that’s the read counts!!
Alannah Miranda
@ahmirand
Screen Shot 2016-02-12 at 1.08.51 PM.png
Olga Botvinnik
@olgabot
that distribution is exactly what it should look like
So you need that column - don’t ignore it
it’s the read counts per gene
the distribution is exactly what it should be
it looks big and crazy because theres some genes that had 10000s of reads mapping to it
the KeyError is like a NameError except in teh dataframe
it can’t find a column named that
so when you ignored that column, yhou no longer have it and you can’t plot it
Alannah Miranda
@ahmirand
Ohhh haha i thought it was an error since the header for that column is the bam file location
Olga Botvinnik
@olgabot
nope - that’s exactlyw hat the column should be called
it’s called that so you know which bam file you used to count features on
Alannah Miranda
@ahmirand
cool, well then in that case in the first notebook I just noticed we were supposed to use the Chr11 subset file for featurecounts. should i go back and change that for this hmwk or is this one okay to use?
Olga Botvinnik
@olgabot
you can use the full dataset
featurecounts is faster than I thought
Alannah Miranda
@ahmirand
okay, great. thank you!!
Olga Botvinnik
@olgabot
you are welcome!
LElmen
@LElmen
@olgabot haha wrong window... please ignore
LElmen
@LElmen
@olgabot Hello again, something is not right with my kallisto script. Is the #PBS -V flag supposed to be empty?
Olga Botvinnik
@olgabot
yes it puts everythign in your environment variables
can you show the output of the .err file ?
LElmen
@LElmen

std.err says Error: Missing read files
Error: need to specify output directory

/var/spool/torque/mom_priv/jobs/4357181.tscc-mgr.local.SC: line 12: --threads: command not found

So it looks like I would have missed --output-dir, but that's in there
Olga Botvinnik
@olgabot
can you show the script?
LElmen
@LElmen
Screen Shot 2016-02-12 at 2.30.07 PM.png
Olga Botvinnik
@olgabot
You need another “\” after the first line
It thinks the first line is one command and it ends
and it starts reading the next line thinking it’s a new command called —threads and there’s nothing called that so it gets confused
computers get confused too :(
LElmen
@LElmen
:smile:
I'll try that.
Thnx
On tscc, q=queued, r=running, c=cancelled, or is c for complete?
Olga Botvinnik
@olgabot
c=compelte
which may have been cancelled by you or it finished
LElmen
@LElmen
ok
LElmen
@LElmen
It makes sh.err and sh.out, but I don't get an output folder. The error message is quite long.
Screen Shot 2016-02-12 at 3.07.08 PM.png
Screen Shot 2016-02-12 at 3.07.19 PM.png
Olga Botvinnik
@olgabot
huh and you’re ucsd-train05 ?
LElmen
@LElmen
Yes
Olga Botvinnik
@olgabot
that’s a really strange error
I haven’t seen that before
okay you specified 8 threads and asked for 8 processors (threads) from TSCC