Error in run_bowtie2.pl

[Jeff Strohm]

Hi there,

I'm trying to run the "Examine Strand Specificity" workflow, with the following command:

./run_bowtie2.pl  [Trinity_on_data_36__Assembled_Transcripts].fasta B5385_S1_R1.fastq B5385_S1_R2.fastq | samtools view -Sb - | samtools sort - -o strandtest.bowtie2.coordSorted.bam

I get the following error:

Can't locate Findbin.pm in @INC (you may need to install the Findbin module) (@INC contains: /usr/local/lib/perl5/site_perl/5.24.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.24.1 /usr/local/lib/perl5/5.24.1/x86_64-linux /usr/local/lib/perl5/5.24.1 .) at ./run_bowtie2.pl line 5.
BEGIN failed--compilation aborted at ./run_bowtie2.pl line 5.

I upgraded to the latest version of Perl (v5.24), but this did not rectify.

Any tips?

Thanks

-Jeff

[Brian Haas]

Hi Jeff,

Which version of Trinity is this?

Attached is the current script. The earlier one might have had a typo in it.

best,

~b

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[Jeff Strohm]

Thanks Brian,

I was running Trinity v2.3.2. I've now upgraded to v 2.4

Now I'm getting a message from bowtie2 related the TBB library:

bowtie2-build: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

I've downloaded TBB and added the directory with the libtbb.so.2 to my path. I've also copied the contents of the lib directory into the bowtie2 directory, but it's not working.

I also tried running the updated run_bowtie2.pl from within the bowtie2 directory and got the following instead: Can't locate Process_cmd.pm in @INC


Gah!

On Monday, March 20, 2017 at 11:27:33 AM UTC-7, Brian Haas wrote:

Hi Jeff,

Which version of Trinity is this?

Attached is the current script. The earlier one might have had a typo in it.

best,

~b

On Mon, Mar 20, 2017 at 1:55 PM, Jeff Strohm <strohm...@gmail.com> wrote:

Hi there,

I'm trying to run the "Examine Strand Specificity" workflow, with the following command:

./run_bowtie2.pl  [Trinity_on_data_36__Assembled_Transcripts].fasta B5385_S1_R1.fastq B5385_S1_R2.fastq | samtools view -Sb - | samtools sort - -o strandtest.bowtie2.coordSorted.bam

I get the following error:

Can't locate Findbin.pm in @INC (you may need to install the Findbin module) (@INC contains: /usr/local/lib/perl5/site_perl/5.24.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.24.1 /usr/local/lib/perl5/5.24.1/x86_64-linux /usr/local/lib/perl5/5.24.1 .) at ./run_bowtie2.pl line 5.
BEGIN failed--compilation aborted at ./run_bowtie2.pl line 5.

I upgraded to the latest version of Perl (v5.24), but this did not rectify.

Any tips?

Thanks

-Jeff

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[Brian Haas]

Hi Jeff,

The bowtie2 folks might be able to help out with those issues.   You might be able to install an older version of bowtie2 that doesn't use that TBB library.

best,

~b

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The Broad Institute
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