Undefined subroutine &RUM::Script::Indexes::isdigit

[rashidma]

Hello everyone, I am working on Ubuntu 18.04 Linux workstation. This is perl 5, version 26, subversion 1 (v5.26.1) built for x86_64-linux-gnu-thread-multi. I installed rum through github. I was trying to install rum indexes as follow- ./rum_indexes --prefix /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/software/RUM/rum_indexes/ -i hg19

It is throwing an error as below -

Possible precedence issue with control flow operator at /home/mamoon/rum/bin/../lib/perl5/RUM/Common.pm line 104. Using the repository located at /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/software/RUM/rum_indexes Undefined subroutine &RUM::Script::Indexes::isdigit called at ./rum_indexes line 138.

Any help is appreciated. Thanks

[brainfood]

Hello Mamoon,

Thank you for your interest in RUM. We currently recommend users try more modern aligners like STAR and GSNAP, since resource limitations have kept us from updating RUM for quite some time. If you still wish to move ahead with RUM, here are a few details about the problem you are encountering.

It looks like RUM is throwing that error because the 'isdigit' function is now deprecated. This function used to be included in perl's POSIX module, so it is not directly part of the RUM codebase. You could probably get around this issue by changing line 138 of the rum/rum_indexes script from if (isdigit($spec)) { to if ($spec =~ m/^\d+$/) {

There are probably other parts of the RUM code that might cause problems with newer versions of perl. So, as I said above, you will be much better off trying to use something like STAR or GSNAP for your RNA-Seq alignment needs. Good luck!

-Nick

[rashidma]

Hello Nick, First of all I am very sorry that I completely forgot to reply to your email.

Thanks a lot for your suggestion to use other aligners. I will try STAR.

By the way, I was inspired by the following article to use RUM. You will be happy to see this article.

"Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis"

Best regards

Mamoon

On Thu, Jan 6, 2022 at 12:41 AM brainfood @.***> wrote:

Hello Mamoon,

Thank you for your interest in RUM. We currently recommend users try more modern aligners like STAR and GSNAP, since resource limitations have kept us from updating RUM for quite some time. If you still wish to move ahead with RUM, here are a few details about the problem you are encountering.

It looks like RUM is throwing that error because the 'isdigit' function is now deprecated. This function used to be included in perl's POSIX module, so it is not directly part of the RUM codebase. You could probably get around this issue by changing line 138 of the rum/rum_indexes script from if (isdigit($spec)) { to if ($spec =~ m/^\d+$/) {

There are probably other parts of the RUM code that might cause problems with newer versions of perl. So, as I said above, you will be much better off trying to use something like STAR or GSNAP for your RNA-Seq alignment needs. Good luck!

-Nick

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Mamoon Rashid, PhD (Bioinformatics)

Associate Research Scientist

Department of Biostatistics and Bioinformatics

King Abdullah International Medical Research Center (KAIMRC) Kingdom of Saudi Arabia