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4.1 years ago
p
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0
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.
