macmanes

[macmanes@br018 ~]$ conda create -n albacore-2.3.1 python=3.6
-bash: conda: command not found
[macmanes@br018 ~]$ module load anaconda
[macmanes@br018 ~]$ conda create -n albacore-2.3.1 python=3.6
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /home/macmanes/.conda/envs/albacore-2.3.1:

macmanes

tmux cheat sheet

(C-x means ctrl+x, M-x means alt+x)

Prefix key

The default prefix is C-b. If you (or your muscle memory) prefer C-a, you need to add this to ~/.tmux.conf:

remap prefix to Control + a

macmanes

from Bio import SeqIO
import sys

##python filter.py file.fasta names.list | tee -a output.fasta

wanted = [line.strip() for line in open(sys.argv[2])]
seqiter = SeqIO.parse(open(sys.argv[1]), 'fasta')
SeqIO.write((seq for seq in seqiter if seq.id in wanted), sys.stdout, "fasta")

macmanes

PRACTICAL EXAM 2

 

Name __________________________________

 

1. Launch a c4.2xlarge instance. (2 points)

macmanes

ubuntu@ip-172-31-43-202:~$ brew update
Already up-to-date.
ubuntu@ip-172-31-43-202:~$ brew doctor
Your system is ready to brew.

brew tap homebrew/science

macmanes

Total BUSCO groups searched: 843
    Phase Two
*** Training Augustus using Single-Copy Complete BUSCOs ***
*** Re-running Augustus with the new metaparameters, number targets: 273 ***
=>	10.0% of predictions performed
=>	25.0% of predictions performed
=>	50.0% of predictions performed
=>	75.0% of predictions performed
=>	100%% of predictions performed

macmanes

java -jar -Xmx600G /share/bin/pilon-1.17.jar --genome jelly.out.fasta \
--frags nygc.mapped.sorted.bam \
--frags hcgs.mapped.sorted.bam \
--output peer_pilon \
--tracks \
--diploid \
--threads 40 \
--verbose

macmanes

java -jar -Xmx600G /share/bin/pilon-1.17.jar --genome jelly.out.fasta \
--frags nygc.mapped.sorted.bam \
--frags hcgs.mapped.sorted.bam \
--output peer_pilon \
--tracks \
--diploid \
--threads 40 \
--verbose

macmanes

Looks like $SELFDIR not working properly.

curl -LO https://bintray.com/artifact/download/blahah/generic/transrate-1.0.2-linux-x86_64.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 27.7M  100 27.7M    0     0  3854k      0  0:00:07  0:00:07 --:--:-- 2382k
macmanes@Pinky:~$

macmanes

using the 'Binary', which looks like it has to be compiled..

The program runs, has obvious fatal errors, still gives the Congratulations! Your job is finished! FML...

$ ./BinPacker -s fq -p pair -l ./sample_test/reads.left.fq -r ./sample_test/reads.right.fq -m RF -k 25 -g 200                                │························································
Processing data...                                                                                                                                                                   │························································
./plugins/fastool/fastool --rev --to-fasta ./sample_test/reads.left.fq >reads.left.fa                                                                                                │························································
./BinPacker: line 180: ./plugins/fastool/fastool: No such file or directory