Question: (Closed) Cuffdiff Error on Galaxy
0
gravatar for p
10 weeks ago by
p0
p0 wrote:

hello I am trying to run cuffdiff on use galaxy server but I keep on running into the same error: error

An error occurred with this dataset:
[03:49:54] Loading reference annotation and sequence.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[03:50:04] Inspecting maps and determining fragment length distributions.
BAM record error: found spliced alignment without XS attribute

BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment without XS attribute

Processed 32333 loci.                       
Performed 24842 isoform-level transcription difference tests
Performed 20708 tss-level transcription difference tests
Performed 19599 gene-level transcription difference tests
Performed 20701 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking
Writing isoform-level count tracking
Writing TSS group-level count tracking
Writing gene-level count tracking
Writing CDS-level count tracking
Writing isoform-level read group tracking
Writing TSS group-level read group tracking
Writing gene-level read group tracking
Writing CDS-level read group tracking
Writing read group info
Writing run info
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

promoters

The following object is masked from ‘package:IRanges’:

promoters

The following object is masked from ‘package:BiocGenerics’:

conditions

Creating database ./cummeRbund.sqlite
Reading Run Info File ./run.info
Writing runInfo Table
Reading Read Group Info  ./read_groups.info
Writing replicates Table
Reading Var Model Info  ./var_model.info
Writing varModel Table
Reading ./genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading ./gene_exp.diff
Writing geneExpDiffData table
Reading ./promoters.diff
Writing promoterDiffData table
Reading ./genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in ./genes.read_group_tracking
Writing geneReplicateData table
Reading ./isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading ./isoform_exp.diff
Writing isoformExpDiffData table
Reading ./isoforms.count_tracking
Reshaping isoform counts table
Recasting
Writing isoform counts table
Reading read group info in ./isoforms.read_group_tracking
Writing isoformReplicateData table
Reading ./tss_groups.fpkm_tracking
Checking the samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading ./tss_group_exp.diff
Writing TSSExpDiffData table
Reading ./splicing.diff
Writing splicingDiffData table
Reading ./tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in ./tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading ./cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading ./cds_exp.diff
Writing CDSExpDiffData table
Reading ./cds.diff
Writing CDSDiffData table
Reading ./cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in ./cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped 
2: attributes are not identical across measure variables; they will be dropped 
3: attributes are not identical across measure variables; they will be dropped 
4: attributes are not identical across measure variables; they will be dropped 
5: attributes are not identical across measure variables; they will be dropped 
6: attributes are not identical across measure variables; they will be dropped 
7: attributes are not identical across measure variables; they will be dropped 
8: attributes are not identical across measure variables; they will be dropped

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under

in the end, I need to find a gene differential FPKM file to identify the differential gene expressed in two conditions.

usegalaxy rna-seq ngs • 95 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by p0

Hello p!

We believe that this post does not fit the main topic of this site.

Please ask Galaxy-related questions over at their support forum: https://help.galaxyproject.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 7 days ago by ATpoint34k
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