Entering edit mode
8.2 years ago
tjdrnjsqpf
▴
10
Hello. I am a student of Chonnam National University in Korea.
I was running this command.
trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl --est_method RSEM hanwoo_cmale_i_r1.genes.results hanwoo_cmale_i_r2.genes.results hanwoo_cmale_i_r3.genes.results
I was faced with this problem
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "ko_KR.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
-reading file: hanwoo_cmale_i_r1.genes.results
-reading file: hanwoo_cmale_i_r2.genes.results
-reading file: hanwoo_cmale_i_r3.genes.results
* Outputting combined matrix.
/home/toolbox/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.matrixperl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "ko_KR.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
CMD: R --vanilla -q < __tmp_runTMM.R 1>&2
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_COLLATE failed, using "C"
3: Setting LC_TIME failed, using "C"
4: Setting LC_MESSAGES failed, using "C"
5: Setting LC_MONETARY failed, using "C"
6: Setting LC_PAPER failed, using "C"
7: Setting LC_MEASUREMENT failed, using "C"
> library(edgeR)
Loading required package: limma
>
> rnaseqMatrix = read.table("matrix.not_cross_norm.fpkm.tmp", header=T, row.names=1, com='', check.names=F)
> 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 /home/toolbox/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl line 98.
Error, CMD: /home/toolbox/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.matrix died with ret 6400 at /home/toolbox/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl line 240.
What should I do to solve the problem?
