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4.9 years ago
1353288408
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/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.