These are chat archives for biom262/biom262-2016

14th
Jan 2016
andersonbrookee
@andersonbrookee
Jan 14 2016 01:50
My jupyter notebook is giving me a bash: line 1: bedtools: command not found error when I hit shift-enter to do exercise 3. Bedtools is installed and working on my terminal which is connected to TSCC, but do I need to somehow install the bedtools module in jupyter too?
Alannah Miranda
@ahmirand
Jan 14 2016 03:07
In the line above your bedtools command input the '''
Whoops I meant to say out the module load biotools
mbaughn
@mbaughn
Jan 14 2016 03:12
 module load biotools
code
andersonbrookee
@andersonbrookee
Jan 14 2016 03:14
thanks!
Alannah Miranda
@ahmirand
Jan 14 2016 03:15
Lol yes thanks @mbaughn haha sorry I was typing on my phone
mbaughn
@mbaughn
Jan 14 2016 03:18
:+1:
Olga Botvinnik
@olgabot
Jan 14 2016 04:38
Yay helping each other out!
If you're making a notebook with a bunch of bedtools stuff you also can do "module load biotools" before your jupyter command and then you'll have bedtools at your disposal without that extra line in each cell
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 04:48
helllo
i think i got everything but I still get funny assertion errors in the notebook
Olga Botvinnik
@olgabot
Jan 14 2016 04:51
Hmm can you paste the full output?
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:04
yes one sec
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-4-503b998b4aba> in <module>()
     34 chr22   51060107        51060383        NFKB    354     .       51060107        51060383        0       1       276,    0,
     35 '''
---> 36 assert exercise1 == answer1

AssertionError:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-7-74056ee90766> in <module>()
     34 chr22   HAVANA  transcript      51220662        51221473        .       -       .       gene_id "ENSG00000079974.13"; transcript_id "ENST00000413505.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "RABL2B"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "RABL2B-011"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000150156.3"; havana_transcript "OTTHUMT00000316616.2";
     35 '''
---> 36 assert exercise2 == answer2

AssertionError:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-10-45dbde82b9d5> in <module>()
     34 chr22   HAVANA  transcript      51221474        51223473        .       -       .       gene_id "ENSG00000079974.13"; transcript_id "ENST00000413505.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "RABL2B"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "RABL2B-011"; level 2; tag "alternative_5_UTR"; tag "mRNA_end_NF"; tag "cds_end_NF"; havana_gene "OTTHUMG00000150156.3"; havana_transcript "OTTHUMT00000316616.2";
     35 '''
---> 36 assert exercise3 == answer3

AssertionError:

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-13-963767923691> in <module>()
     34 chr22   HAVANA  transcript      51021040        51021316        .       +       .       gene_id "ENSG00000205559.3"; transcript_id "ENST00000380711.3"; gene_type "antisense"; gene_status "NOVEL"; gene_name "CHKB-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "CHKB-AS1-001"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000150208.1"; havana_transcript "OTTHUMT00000316839.1";
     35 '''
---> 36 assert exercise4 == answer4

AssertionError:
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-16-4498ca8e7372> in <module>()
     35 '''
     36 
---> 37 assert exercise5 == answer5

AssertionError:
LElmen
@LElmen
Jan 14 2016 05:09
Hi, I'd like to see what the hg19.genome file contains, but when I use head or tail nothing happens. ?
[ucsd-train05@tscc-login2 data]$ head hg19.genome
[ucsd-train05@tscc-login2 data]$
[ucsd-train05@tscc-login2 data]$ tail hg19.genome
[ucsd-train05@tscc-login2 data]$ cd hg19.genome
-bash: cd: hg19.genome: Not a directory
Olga Botvinnik
@olgabot
Jan 14 2016 05:10
You may have overwritten it
LElmen
@LElmen
Jan 14 2016 05:10
Oh.
Olga Botvinnik
@olgabot
Jan 14 2016 05:10
What is "ls -lh hg19.genome"
And "git status"
@bmlewis-UCSD
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:11
yes
Olga Botvinnik
@olgabot
Jan 14 2016 05:11
@bmlewis-UCSD you're doing this on tscc I presume?
LElmen
@LElmen
Jan 14 2016 05:11
[ucsd-train05@tscc-login2 data]$ ls -lh hg19.genome
-rw-r--r-- 1 ucsd-train05 biom262-group 0 Jan 11 23:18 hg19.genome
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:11
yes
in browser
local lhost
Olga Botvinnik
@olgabot
Jan 14 2016 05:12
It's "wc" that's the problem
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:12
me?
Olga Botvinnik
@olgabot
Jan 14 2016 05:13
I don't think you've updated your notebook to the latest hw - there should be another line above the assert
@LElmen yes the file is empty - size is zero
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:13
how can i do that without losing the bits that i added
Olga Botvinnik
@olgabot
Jan 14 2016 05:13
The instructions describe how to solve the merge conflicts
Which will arise when you've made changes to a line that conflicts with the server (eg here you did your homework)
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:14
ok thanks... i was wondering why some of the expected wc 's seemed off
Olga Botvinnik
@olgabot
Jan 14 2016 05:15
@LElmen do "git status" then "git checkout -- hg19.genome"
Thst should be a double dash
When you type git status it'll give you that command as a hint to "discard your changes"
Then do "git status" and "ls -lh" again to convince yourself that the file is nonempty
LElmen
@LElmen
Jan 14 2016 05:16
I just wrote head - there is contents :-)
Olga Botvinnik
@olgabot
Jan 14 2016 05:17
@bmlewis-UCSD Yeah that's my bad.. The Mac implementation of wc adds spaces at the beginning but the Linux one doesn't
Yay!
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:18
ok i am looking for how to update
Olga Botvinnik
@olgabot
Jan 14 2016 05:18
Do the git and ls stuff too to get the commands into your fingers
It's in the homework.ipynb - ctrl F for "update"
Okay I'm going to bed... Gave lab meeting today so I'm very tired
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 05:19
ok thanks
LElmen
@LElmen
Jan 14 2016 06:31
Hi all, I'm on exercise 3. Why does my output file only match the first line of the given answer (written in red in the cell under)? The input file (gencode.v19.annotation.chr22.transcript.gtf) from exercise 2 matches the answer given in exercise2.
[ucsd-train05@tscc-login2 data]$ wc -l gencode.v19.annotation.chr22.transcript.promoter.gtf
4459 gencode.v19.annotation.chr22.transcript.promoter.gtf
I get the expected 4459 lines.
andersonbrookee
@andersonbrookee
Jan 14 2016 07:24
@LElmen , you need to take positive/negative strand into effect. It's in the documentation for flanking how you do that.
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 16:44
@olgabot thanks for the help got all my assertion errors fixed and I think I am done
bmlewis-UCSD
@bmlewis-UCSD
Jan 14 2016 18:03
jk I fixed them all except I still get one for exercise 5
Brian Reilly
@bmreilly
Jan 14 2016 18:07
did you use the -s flag?
jmeinst
@jmeinst
Jan 14 2016 20:10
Hi Olga,
I'm having an issue that my python kernel is dead. Jamison tried to help me today but it didn't work. I've tried conda update conda and trying to update my ipython kernel and it still says the kernel is dead on tscc. Do you have any idea how I can fix this? Should I remove and reinstall anaconda?
afsheenbanisadr
@afsheenbanisadr
Jan 14 2016 21:24
Hey Olga I get a truncated version of the partner portion of the HW
blob
Just FYI this may affect what people turn in
jmeinst
@jmeinst
Jan 14 2016 21:34
For anyone experiencing the problem I was having with a dead kernel can fix it by doing the follow: 1. make sure you're using a port that no one else is using. It's okay to change your port. If they reassign you to a different port make sure you use that port on your home computer when tunneling. 2. Run the command rm -rf .ipython/ to get rid of any "zombie" processes that may be going on in the background. This worked for me.
mbaughn
@mbaughn
Jan 14 2016 21:36
Jamison M McCorrison
@bioh4x
Jan 14 2016 21:41
@jmeinst Awesome news! Thank you for posting your fix.
jmeinst
@jmeinst
Jan 14 2016 22:53
Glad it helped some of you!
Olga Botvinnik
@olgabot
Jan 14 2016 23:00
@afsheenbanisadr did you do the update for the hw?