ERROR for Trinity abundance_estimates_to_matrix.pl

Question

[nasreenbano91]

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.

[WouterDeCoster]

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Answer 1

[WouterDeCoster]

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.