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I'm trying to update our Ubuntu server installation of 1.9.0 to 1.9.1 and banging my head with the following error:
```
Exception:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/…
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```
Starting program: /home/buckstabu/dev/dhewm3/build/dhewm3 +set r_fullscreen 0
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1…
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Bug in plot.credibleshiftset
Chokes when some options to plot.bammdata are passed indirectly
Eg passing lwd gives:
Error in assignColorBreaks(cset.bamm$dtrates$rates, spex = spex, ...) :
unused …
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Expects an int according to argparser, but then later requires it to be a string. Presumably never tested code.
Also not documented - needs an example in the
Possibly a hangover bug from makeSam (a…
wwood updated
10 years ago
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Calling bamm make causes a system crash if bwa is not on the system path:
/bin/sh: 1: bwa: not found
Traceback (most recent call last):
File "/srv/sw/BamM/1.0.0/bin/bamm", line 433, in
doWork(…
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I have a dream, of estimating coverage using pileup columns in the 60-90% range.
Currently this
- cannot be specified on the bamm cmdline (-r takes a float)
- isn't given to the C code (the bamInfo s…
wwood updated
10 years ago
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bamm make -d Isca_2_Bulk1ml_CLC_contigs.gt1000.fa -c ISCA-2-Bulk1ml_all_R1.fastq.gz ISCA-2-Bulk1ml_all_R2.fastq.gz -t 10 -K
Eventually runs (with 1010G of memory):
samtools sort -m 1010G - /srv/proj…
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Hey,
I've noticed bamm taking a decent amount of memory (100GB+ before I brought down the hammer) when running through a bam file with large numbers of contigs (~8 million), using outlier mode.
One …
wwood updated
10 years ago
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Need to make it easier for users to change color map for plot.bammdata. The current system works great for some trees, but the nonlinear color mapping can produce weird artifacts when applied to trees…
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I am getting
terminate called after throwing an instance of 'std::system_error'
what(): Enable multithreading to use std::thread: Operation not permitted
from a clean build using ubuntu 14.04 and…