Open mr-c opened 10 years ago
Same with khmer v1.1
@ctb @luizirber Any ideas? I'm running it using the ancient 'beacon' AMI right now.
On Tue, Aug 05, 2014 at 12:16:39PM -0700, Michael R. Crusoe wrote:
@ctb @luizirber Any ideas? I'm running it using the ancient 'beacon' AMI right now.
Well, it's irrelevant to khmer itself, since it happens well after any khmer scripts. I'll fix it later.
--t
https://github.com/ged-lab/khmer-protocols/issues/129#issuecomment-51245527
C. Titus Brown, ctb@msu.edu
The command
for i in [1-8]-*.txt.sh
do
bash $i
done
Completes successfully using the ancient ami-c17ec8a8 AMI with one twist: I had to run sed -i 's/archive/old-releases/g' /etc/apt/sources.list
first.
The output from assemstats3 is a bit off:
root@ip-10-231-135-216:~/khmer-protocols/mrnaseq# /usr/local/share/khmer/sandbox/assemstats3.py 500 /mnt/work/trinity_out_dir/Trinity.fasta
** cutoff: 500
N sum max filename
35 61061 4449 /mnt/work/trinity_out_dir/Trinity.fasta
Should be
** cutoff: 500
N sum max filename
76 134259 4452 /mnt/work/trinity_out_dir/Trinity.fasta
according to https://github.com/ged-lab/literate-resting/tree/master/kp
The command grep "zinc transporter" /mnt/blast/trinity.x.mouse | wc -l
returns 24.
This is still an issue.