#!/usr/bin/env python
# coding: utf-8

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get_ipython().run_cell_magic('bash', '', 'echo "TODAY\'S DATE:"\ndate\necho "------------"\necho ""\nlsb_release -a\necho ""\necho "------------"\necho "HOSTNAME: "; hostname \necho ""\necho "------------"\necho "Computer Specs:"\necho ""\nlscpu\necho ""\necho "------------"\necho ""\necho "Memory Specs"\necho ""\nfree -mh\n')


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get_ipython().run_cell_magic('bash', '', 'mkdir /home/sam/analyses/20171130_oly_pbjelly\n')


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ls /home/sam/analyses/20171120_oly_pbjelly/


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ls /home/sam/analyses/20171130_oly_pbjelly/


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get_ipython().run_cell_magic('bash', '', 'cp /home/sam/analyses/20171120_oly_pbjelly/Protocol.xml /home/sam/analyses/20171130_oly_pbjelly/\n')


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get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\n')


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get_ipython().run_cell_magic('bash', '', "sed -i 's/20171120_oly_pbjelly/20171130_oly_pbjelly/g' /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\n")


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get_ipython().run_cell_magic('bash', '', 'cat /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\n')


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get_ipython().run_cell_magic('bash', '', 'source /home/shared/PBSuite_15.8.24/setup.sh\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\ntime python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml\n')


# #### Well, Firefox crashed while the command above was running (20180103). However, PB Jelly is still running. I'll report on output once it has completed.

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get_ipython().run_cell_magic('bash', '', 'source ~/.bashrc\nsource ~/.bash_aliases\nemailme\n')


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get_ipython().run_cell_magic('bash', '', 'ls -lthr /home/sam/analyses/20171130_oly_pbjelly/\n')


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get_ipython().run_cell_magic('bash', '', '# Count the number of ">" (i.e. scaffolds) in the output file\ntr -cd \\> < /home/sam/analyses/20171130_oly_pbjelly/jelly.out.fasta | wc -c\n')


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get_ipython().run_cell_magic('bash', '', 'time cp -pR /home/sam/analyses/20171130_oly_pbjelly/ /mnt/owl/Athaliana/\nsource ~/.bashrc\nsource ~/.bash_aliases\nemailme\n')


# Used ```sudo``` outside of notebook for copying.

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get_ipython().run_cell_magic('bash', '', 'ls -ltrh /mnt/owl/Athaliana/20171130_oly_pbjelly/\n')


# Started this notebook again to run Quast.

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get_ipython().system('python /home/sam/software/quast-4.5/quast.py  -t 24  /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta')


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get_ipython().run_cell_magic('bash', '', 'cat quast_results/results_2018_01_16_09_35_09/report.txt\n')


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get_ipython().run_cell_magic('bash', '', 'cp -pR quast_results/results_2018_01_16_09_35_09/ /mnt/owl/Athaliana/quast_results/\n')


# #### Needed to use ```sudo``` to cp, so did that outside of notebook.

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get_ipython().run_cell_magic('bash', '', 'ls /mnt/owl/Athaliana/quast_results/results_2018_01_16_09_35_09/\n')


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