tgarvin
commented
7 years ago Does that library have a very low number of mapped reads compared to the others?
Sent from my iPhone
On Aug 2, 2017, at 11:51 AM, Richard Corbett notifications@github.com<mailto:notifications@github.com> wrote:
Hi there,
I'm setting up a local install of ginko and running a set of just over 900 single cell libraries. After installing all the required libraries I had to make a small change to the code:
line 25 of analyze.sh is looking for a folder called "genomes" this isn't in my install so I took it out and got much farther.
Now I get to the part when lots of .jpegs are being created and I get an error that I have narrowed down to this location:
/opt/ginkgo/scripts/process.R /opt/ginkgo/genomes/hg19 /opt/ginkgo/uploads/CIC1 status.xml data 0 variable_100000_150_bwa ward.D2 euclidean 1 refDummy.bed_mapped 0 ploidyDummy.txt 1 0 Loading required package: amap Loading required package: methods
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowessError in clip(tu[1], mean(temp) - (diff(reads$mids)/2), tu[3], tu[4]) : invalid 'x2' argument In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted
I get this error after getting though 102 libraries for which I get lots of pretty .jpeg images.
Looking in the status.xml file I am able to narrow this down to happening on just one of my libraries. That particular library doesn't looking very different from the others.
Do you have any suggestions I could try ?
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RichardCorbett
Hi there,
I'm setting up a local install of ginko and running a set of just over 900 single cell libraries. After installing all the required libraries I had to make a small change to the code:
line 25 of analyze.sh is looking for a folder called "genomes" this isn't in my install so I took it out and got much farther.
Now I get to the part when lots of .jpegs are being created and I get an error that I have narrowed down to this location:
I get this error after getting though 102 libraries for which I get lots of pretty .jpeg images.
Looking in the status.xml file I am able to narrow this down to happening on just one of my libraries. That particular library doesn't looking very different from the others.
Do you have any suggestions I could try ?