trouble abundance_estimates_to_matrix.pl (trinity2.4.0)

Question

[1353288408]

/opt/software/trinityrnaseq-Trinity-v2.4.0/util/abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix transyyy ../*.isoforms.results

Output

-reading file: ../a.isoforms.results
-reading file: ../b.isoforms.results


* Outputting combined matrix.

/opt/software/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix transyyy.TPM.not_cross_norm > transyyy.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2 
> library(edgeR)
Loading required package: limma
> 
> rnaseqMatrix = read.table("transyyy.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)))
> exp_study = calcNormFactors(exp_study)
Error in calcNormFactors.default(object = object$counts, lib.size = object$samples$lib.size,  : 
  NA counts not permitted
Calls: calcNormFactors ... calcNormFactors.DGEList -> calcNormFactors -> calcNormFactors.default
Execution halted
Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (256)  at /opt/software/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/run_TMM_scale_matrix.pl line 99.
Error, CMD: /opt/software/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix transyyy.TPM.not_cross_norm > transyyy.TMM.EXPR.matrix died with ret 6400 at /opt/software/trinityrnaseq-Trinity-v2.4.0/util/abundance_estimates_to_matrix.pl line 297.

Answer 1

[h.mon]

Please put some effort at:

1) describing your problem, not just copying and pasting code and messages,

2) formatting your post,

3) reading the error message carefully:

Error in calcNormFactors.default(object = object$counts, lib.size = object$samples$lib.size,  : 
  NA counts not permitted
  

4) searching for a solution

https://groups.google.com/forum/#!topic/trinityrnaseq-users/65i4qgprFT0