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ERROR for Trinity abundance_estimates_to_matrix.pl

Hello,

Trying to run abundance_estimates_to_matrix.pl

abundance_estimates_to_matrix.pl --est_method RSEM --out_prefix /home/nbri/nasreen/muku/matrix /home/nbri/nasreen/muku/RSEM_M1.genes.results /home/nbri/nasreen/muku/RSEM_M2.genes.results

I get this:

-reading file: /scratch/sbag/nasreen/mukuna/align11/RSEM_M11.genes.results
-reading file: /scratch/sbag/nasreen/mukuna/align2/RSEM_M2.genes.results

* Outputting combined matrix.

/app/setups/trinityrnaseq-2.2.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix Trinity_matrix.TPM.not_cross_norm > Trinity_matrix.TMM.EXPR.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2
sh: R: command not found

Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2  died with ret (32512)  at /app/setups/trinityrnaseq-2.2.0/util/support_scripts/run_TMM_scale_matrix.pl line 99.
Error, CMD: /app/setups/trinityrnaseq-2.2.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix Trinity_matrix.TPM.not_cross_norm > Trinity_matrix.TMM.EXPR.matrix died with ret 6400 at /app/setups/trinityrnaseq-2.2.0/util/abundance_est
imates_to_matrix.pl line 297.

Any ideas what the issue could be? Thanks.

r next-gen rna-seq software-error
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updated by Ram Ram • written by nasreenbano91 • nasreenbano91

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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written by WouterDeCoster WouterDeCoster

1 answer

The error message exactly tells you what is wrong. Your program cannot find the R executable. Make sure R is installed and the executable is in $PATH.

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written by WouterDeCoster WouterDeCoster

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