Help with error during building an expression matrix

usegalaxy.org support
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1

Hi, i am trying to build a expression matrix on galaxy platform but ending up with Fatal error: Exit code 25 () and couldn’t able to sort out the error. my input data is two abundance estimate output with tpm and fpkm values. it is showing a Common Potential Problem could be that the tool was executed with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices. (still i am not able to figure out what is wrong with the input file. please help.

-reading file: isoforms328
-reading file: isoforms329

  • Outputting combined matrix.

/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q < RSEM.isoform.TPM.not_cross_norm.runTMM.R 1>&2

library(edgeR)
Loading required package: limma

rnaseqMatrix = read.table(“RSEM.isoform.TPM.not_cross_norm”, header=T, row.names=1, com=‘’, check.names=F)
rnaseqMatrix = as.matrix(rnaseqMatrix)
rnaseqMatrix = round(rnaseqMatrix)
exp_study = DGEList(counts=rnaseqMatrix, group=factor(colnames(rnaseqMatrix)))
Error in .isAllZero(counts) : counts must be positive finite values
Calls: DGEList → .isAllZero
Execution halted
Error, cmd: R --no-save --no-restore --no-site-file --no-init-file -q < RSEM.isoform.TPM.not_cross_norm.runTMM.R 1>&2 died with ret (256) at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/util/support_scripts/run_TMM_scale_matrix.pl line 105.
Error, CMD: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/opt/trinity-2.9.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.TMM.EXPR.matrix died with ret 6400 at /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-03aa6da237310bbe9f60ff3faf43ac3ceb173e3e63cc74bd3f93dd6d9587c3bd/bin/abundance_estimates_to_matrix.pl line 385.

2

Hello,

I just ran into this issue and was wondering if you ever got this resolved or if you decided to go a different route with your analysis?

Thank you!
LB