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
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/