malarkey73 / bash Goto Github PK

Hi,
I was successfully able to map the raw file using the command given in the 4Cseqpipe manual. However, upon using the command:
perl 4cseqpipe.pl -nearcis -calc_from 32000000 -calc_to 32300000 -stat_type median -trend_resolution 5000 -ids 1 -figure_fn example.png
I am only able to generate 1.nearcis.cover.txt in /tables but the command does not generate any other file . also, there is no figure generated in /figures directory. i get no error! i get this instead:
Analyzing coordinates 32000000 - 32300000, ID(s) 1
Creating near-cis plots for ID(s) 1

Please help! i've been stuck here for more than a month now. I've tried everything i could think of.

Thank you.
Sanaa

Hi:
I am trying to use 4Cseqpipe to map my data and find that it can work well in my virtualbox but can not work in server. Because my data is too large to run on my virtualbox so I have to move to server.
I can generate raw file but can not map properly. there is no error reminder, but seems like just not go to 4Cmapper and cannot produce files. The code is like this:

> $ perl 4cseqpipe.pl -map -ids 3 -trackset_name fam56b_public_h1 -binsize 1000 -trackdb_root /home/xzhouaw/4cseqpipe/hg19_trackdb -rawdir /home/xzhouaw/4cseqpipe/rawdata
 will invoke the 4C mapper for experiment id 3 - this can take a while...
> $ 

Please help me with this situation~ It seems something wrong when running in cluster but I don't know why

Hi, I am running 4cseqpipe and I encountered a problem.

I successfully generated a trackbd, a raw file, but when I used that raw file to do mapping, there was always an error message:

will invoke the 4C mapper for experiment id 1 - this can take a while...
../src/TGLException.cpp(33): Raw file rawdata/T2D_F_V1_raw_convert_qual.txt contains sequences of unequal length
scripts/4cmap.sh: line 5: 10930 Aborted                 bin/4cMapper $*

It seems that some of the symbols in the Phred quality column were regarded as comment symbol, so the lines were not read in.

How can I solve this problem? Many thanks.