Olga Botvinnik olgabot

Commencement: June 17th, 2017
- Rent regalia
- Register for All-campus Commencement (w/ Dalai Lama)
- Register for grad commencement (Hooding, name is read)
Making appointments for formatting
- Preliminary formatting appointment (before defense)
  - Suggest: a month before
- Final: submitting, filing
  - Last two weeks are reserved for final appointments only
Spring 2017 degree

	[obotvinnik@tscc-1-51 ~]$ export PYTHONPATH=$HOME/anaconda/lib/python2.7/site-packages/:$PYTHONPATH
	[obotvinnik@tscc-1-51 ~]$ echo $PYTHONPATH
	/home/obotvinnik/anaconda/lib/python2.7/site-packages/:/opt/sdsc/lib/:/opt/scar/lib/::/home/obotvinnik/local/lib/python2.7/site-packages/
	[obotvinnik@tscc-1-51 ~]$ time ~/anaconda/bin/runipy /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se.ipynb /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se_runipy_output.ipynb
	02/07/2017 08:23:59 AM INFO: Reading notebook /projects/ps-yeolab/obotvinnik/singlecell_pnms/notebooks/01_notebooks/00_chronological_order/041_translate_isoforms_to_protein_products_for_runipy_se.ipynb
	Traceback (most recent call last):
	File "/projects/ps-yeolab/software/Anaconda_2.0.1_150511/lib/python2.7/runpy.py", line 151, in _run_module_as_main
	mod_na

	(outrigger) ➜ outrigger git:(merge_exon_finding_and_junction_adjacencies) ✗ python -m pdb outrigger/commandline.py index --sj-out-tab outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/originals/CAV_LP_Ipsi_tdTpos_cell_1*SJ.out.tab --gtf outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf --output $OUTPUT
	> /Users/olga/workspace-git/outrigger/outrigger/commandline.py(3)<module>()
	-> import argparse
	(Pdb) c
	2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output ...
	2017-01-04 12:41:14 Done.
	2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output/index ...
	2017-01-04 12:41:14 Done.
	2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output/index/gtf ...
	2017-01-04 12:41:14 Done.

	# .bash_profile

	# Source global definitions
	if [ -f /etc/bashrc ]; then
	. /etc/bashrc
	fi

	# User specific aliases and functions

	#PATH=/home/obotvinnik/bin/jre1.7.0_07/bin:/home/obotvinnik/packages/java-genomics-toolkit:/home/obotvinnik/packages/epd-7.3-2-rh3-x86_64/bin:$HOME/bin:$PATH:$HOME/packages/weblogo

	((py3k)) [obotvinnik@tscc-login2 fastq_dump]$ fastq-dump --gzip --split-files /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/SRR2140205.sra --outdir /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/
	2016-07-28T15:53:29 fastq-dump.2.5.4 err: name not found while resolving tree within virtual file system module - failed /oasis/tscc/scratch/obotvinnik/external_singlecell/tasic2015/1645630/SRR2140205.sra

	=============================================================
	An error occurred during processing.
	A report was generated into the file '/home/obotvinnik/ncbi_error_report.xml'.
	If the problem persists, you may consider sending the file
	to '[email protected]' for assistance.
	=============================================================