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.
