DEXSeq error message on glmnb.fit

Question: DEXSeq error message on glmnb.fit

3.6 years ago by

Taiwan

cwchen123 • 20 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 • 1.0k views

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modified 3.6 years ago • written 3.6 years ago by cwchen123 • 20

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

ADD REPLY • link written 3.6 years ago by Devon Ryan • 1.9k

The version of DEXSeq is 1.6

ADD REPLY • link written 3.6 years ago by cwchen123 • 20

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 REPLY • link written 3.6 years ago by Bjoern Gruening ♦ 5.1k

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 REPLY • link written 3.6 years ago by cwchen123 • 20

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

ADD REPLY • link written 3.6 years ago by Bjoern Gruening ♦ 5.1k

@cwchen123 can you provide me the log file.

ADD REPLY • link written 3.6 years ago by vipin • 20

3.6 years ago by

cwchen123 • 20

Taiwan

cwchen123 • 20 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 COMMENT • link written 3.6 years ago by cwchen123 • 20

3.6 years ago by

vipin • 20

United States

vipin • 20 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 COMMENT • link written 3.6 years ago by vipin • 20

3.6 years ago by

cwchen123 • 20

Taiwan

cwchen123 • 20 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 COMMENT • link written 3.6 years ago by cwchen123 • 20

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