Error:abundance_estimates_to_matrix.pl [.isAllZero(counts) : counts must be positive finite values]

Question

[jieandze1314]

Hi guys, I'm doing the abundance_estimates_to_matrix with 6 RSEM.genes.results. But I met a problem, the error info as follows:

-reading file: SS_1/RSEM.genes.results
-reading file: SS_2/RSEM.genes.results
-reading file: SS_3/RSEM.genes.results
-reading file: XXCAD_1/RSEM.genes.results
-reading file: XXCAD_2/RSEM.genes.results
-reading file: XXCAD_3/RSEM.genes.results


* Outputting combined matrix.

/home/genek/miniconda3/opt/trinity-2.4.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix genes.TPM.not_cross_norm > genes.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2 
> library(edgeR)
Loading required package: limma
> 
> rnaseqMatrix = read.table("genes.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 --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (256)  at /home/genek/miniconda3/opt/trinity-2.4.0/util/support_scripts/run_TMM_scale_matrix.pl line 99.
Error, CMD: /home/genek/miniconda3/opt/trinity-2.4.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix genes.TPM.not_cross_norm > genes.TMM.EXPR.matrix died with ret 6400 at /home/genek/miniconda3/opt/trinity-2.4.0/util/abundance_estimates_to_matrix.pl line 297.
nohup.out (END)

[jieandze1314]

I don't know how to solve this: Error in .isAllZero(counts) : counts must be positive finite values

Answer 1

[qzhang24]

Hi, did you solve the problems? I met with the same problems. I'd appreciate your reply.