Cuffdiff Error on Galaxy
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Entering edit mode
19 months ago
p • 0

hello , I was doing cuffdiff on use galaxy server, I don't know why this error is coming. I need to find differentially expressed genes in two conditions. Error Details Execution resulted in the following messages:

Fatal error: Exit code 1 () Fatal error: Matched on error Tool generated the following standard error:

[11:01:50] Loading reference annotation and sequence. Warning: No conditions are replicated, switching to 'blind' dispersion method [11:02:00] Inspecting maps and determining fragment length distributions. BAM record error: found spliced alignment without XS attribute

.. 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: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

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

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit

Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 Loading required package: fastcluster

Attaching package: ‘fastcluster’

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

hclust

Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid

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 Error in sqliteSendQuery(con, statement, bind.data) : error in statement: database is locked Error in sqliteSendQuery(con, statement, bind.data) : error in statement: database is locked Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery -> .Call Execution halted

error RNA-Seq galaxy cuffdiff • 398 views
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Having two similar post is a bit confusing, and most users here don't appreciate that. Cuffdiff Error on Galaxy

Even though you use galaxy, you can still try to solve it yourself. Galaxy is just wrapper around the command line.

I am no expert but I think if you want an answer on this forum you only need to ask about the error itself. Did you tried something yourself to solve it? maybe this can help https://groups.google.com/forum/#!topic/rna-star/0Cq51RlyJ5g

If you think it is galaxy specific you can post your question also here: https://help.galaxyproject.org/

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