Question: Error while running cuffdiff "Fatal error: Exit Code 1()"
0
gravatar for rkp21
24 months ago by
rkp2120
rkp2120 wrote:

Hello,

I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18170/#18221). As those issues have been solved, I still have not had a successful cuffdiff run. I don't have any issues with alignment (HISAT) or with cufflinks. Now I am getting the error message below:

Fatal error: Exit code 1 () [11:24:49] Loading reference annotation and sequence. [11:25:16] Inspecting maps and determining fragment length distributions. [11:43:30] Modeling fragment count overdispersion. [11:45:36] Modeling fragment count overdispersion. [11:47:38] Modeling fragment count overdispersion. [11:49:39] Modeling fragment count overdispersion. Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 42703529.80 Number of Multi-Reads: 3564982 (with 6645107 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 42230697.93 Number of Multi-Reads: 3424450 (with 6219883 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 20141604.67 Number of Multi-Reads: 1551264 (with 2839564 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 21211516.88 Number of Multi-Reads: 1661089 (with 3142414 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 19263999.22 Number of Multi-Reads: 1766327 (with 3305783 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 45542494.93 Number of Multi-Reads: 3818029 (with 7085734 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 29138141.70 Number of Multi-Reads: 2264781 (with 4252556 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 38649015.30 Number of Multi-Reads: 3225526 (with 5972848 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 33531917.27 Number of Multi-Reads: 2578694 (with 4741620 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 28441169.60 Number of Multi-Reads: 2202194 (with 4050384 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 32972494.27 Number of Multi-Reads: 2410824 (with 4446162 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 Map Properties: Normalized Map Mass: 30863522.25 Raw Map Mass: 33191740.13 Number of Multi-Reads: 2511235 (with 4681720 total hits) Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 [11:51:51] Calculating preliminary abundance estimates Processed 22345 loci.
[13:25:16] Learning bias parameters. [13:41:10] Testing for differential expression and regulation in locus. Processed 22345 loci.
Performed 163265 isoform-level transcription difference tests Performed 99953 tss-level transcription difference tests Performed 82157 gene-level transcription difference tests Performed 117959 CDS-level transcription difference tests Performed 37519 splicing tests Performed 15147 promoter preference tests Performing 30113 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':

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
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 Reading Run Info File ./run.info Writing runInfo Table Reading Read Group Info ./read_groups.info Writing replicates Table Error in sqliteSendQuery(con, statement, bind.data) : rsqlite_query_send: could not execute: UNIQUE constraint failed: replicates.rep_name Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery -> .Call Execution halted

It seems as though the error seems to happen in the generation of the sqlite database? I am not sure what I can change to fix this issue. Would running cuffquant before cuffdiff help? I sent this error to the galaxy admins, but I thought I would ask here too.

ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by rkp2120
0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The galaxy-dev@lists.galaxyproject.org mailing list is a good place to ask this question, and it is best to have that discussion in one place.

Many in the Galaxy community were away at the GCC conference this last week and may still be in travel home. They will respond once back online and working again.

Take care, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k
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