Question: DEXSeq error message on glmnb.fit
0
gravatar for cwchen123
2.7 years ago by
cwchen12320
Taiwan
cwchen12320 wrote:

When I tried DEXSeq on Galaxy on the server of my lab, the DEXSeq session halt and
showed the following error message: 

Error in glmnb.fit(mm, y, initialGuess, mf$offset, start = start) :
  All weights must be positive
Error in glmnb.fit(mm, y, initialGuess, mf$offset, start = start) :
  All weights must be positive
Error in fitDispersionFunction(ecs) :
  no CR dispersion estimations found, please first call estimateDispersions function

I tried Google but cannot figure out the real problem.  Any further suggestion?

dexseq galaxy rna-seq • 556 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by cwchen12320

What version of DEXseq is that using? The fitDispersionFunction() function is deprecated and has been for a while...

ADD REPLYlink written 2.7 years ago by Devon Ryan1.8k

The version of DEXSeq is 1.6

ADD REPLYlink written 2.7 years ago by cwchen12320

Can you point us to the wrapper your are using? At the bottom of your tool should be a link to a Tool Shed repo. If we are lucky it's my wrapper and we can fix it.

ADD REPLYlink written 2.7 years ago by Bjoern Gruening4.8k

The dexseq-hts repo: https://toolshed.g2.bx.psu.edu/view/vipints/deseq_hts

Synopsis: A Galaxy wrapper for DESeq version 1.12, DESeq2 version 1.0.19 and DEXSeq version 1.6

Thanks for your reply.

ADD REPLYlink written 2.7 years ago by cwchen12320

Ok, not mine but I will poke Vipin! :)

ADD REPLYlink written 2.7 years ago by Bjoern Gruening4.8k

@cwchen123 can you provide me the log file. 

ADD REPLYlink written 2.7 years ago by vipin20
0
gravatar for cwchen123
2.7 years ago by
cwchen12320
Taiwan
cwchen12320 wrote:

I'm not sure if this is the right file.  Check it out

DEXseq-hts.sh: Oqtans http://galaxy.cbio.mskcc.org Galaxy wrapper for the DEXSeq version 1.6.0.

DEXSeq: Detecting differential usage of exons from RNA-seq data.

%%%%%%%%%%%%%%%%%%%%%%%
% 1. Data preparation %
%%%%%%%%%%%%%%%%%%%%%%%

extra file path /home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files
load the genome annotation in GFF file
genome annotation stored in /tmp/tmp.tRBpcFbcPH

%%%%%%%%%%%%%%%%%%%%
% 2. Read counting %
%%%%%%%%%%%%%%%%%%%%

/tmp/tmp.v3DFzPqDRQ



conuted condition 1



conuted condition 2
counted reads map to each exon.

%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 3. Differential testing %
%%%%%%%%%%%%%%%%%%%%%%%%%%%

cat /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/dexseq-hts_1.0/galaxy/./../src/run_DEXseq.R | /usr/bin/R --slave --args /tmp/tmp.v3DFzPqDRQ /home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files /tmp/tmp.tRBpcFbcPH /home/galaxy/galaxy-dist/database/files/006/dataset_6693.dat 2
[1] "1__vs__2"
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6609
                                                                                       1.1493244
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6620
                                                                                       1.1114541
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6630
                                                                                       1.2009311
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6641
                                                                                       0.9865754
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6651
                                                                                       1.3509600
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6604
                                                                                       0.9340099
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6614
                                                                                       1.0493407
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6625
                                                                                       0.7390116
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6636
                                                                                       0.8750085
/home/galaxy/galaxy-dist/database/job_working_directory/004/4227/dataset_6693_files/dataset_6646
                                                                                       1.3140858

 

ADD COMMENTlink written 2.7 years ago by cwchen12320
0
gravatar for vipin
2.7 years ago by
vipin20
United States
vipin20 wrote:
sorry for the super delay from my side. Can you please check the content of /tmp/tmp.v3DFzPqDRQ file. Is that relevant to your experiment setup?
ADD COMMENTlink written 2.7 years ago by vipin20
0
gravatar for cwchen123
2.7 years ago by
cwchen12320
Taiwan
cwchen12320 wrote:

The content of /tmp/tmp.v3DFzPqDRQ file is empty.  However, tmp.v3DFzPqDRQ_CONDITIONS.tab show the following message:

        condition       libType
dataset_6609    1       PE
dataset_6620    1       PE
dataset_6630    1       PE
dataset_6641    1       PE
dataset_6651    1       PE
dataset_6604    2       PE
dataset_6614    2       PE
dataset_6625    2       PE
dataset_6636    2       PE
dataset_6646    2       PE

I hope the message helpful.

 
ADD COMMENTlink written 2.7 years ago by cwchen12320
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