Can't locate Common.pm at filtering step

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Cai Qi

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Oct 5, 2020, 6:31:08 PM10/5/20

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I am in the process of using PAR-Clip protocol on the sample data. I use anaconda to install cutadapt, perl, perl-math-cdf. I can module load bwa from the computation center server.

I have downloaded the cziplib and CTK and do the :

export PERL5LIB=/usr/local/lib/czplib

PATH=$PATH:~/CTK_toolkit/ctk/ and export PATH.

After these, I downloaded the PUM PAR-CLIP dataset and do the filtering using bash.

srun -c 16 --mem-per-cpu=4096M -n 1 -N 1 -p bigmem2 bash fastq_filter.sh

I got error:

srun: job 5751660 queued and waiting for resources

srun: job 5751660 has been allocated resources

Can't locate Common.pm in @INC (you may need to install the Common module) (@INC contains: /software/perl-5.24.1-el7-x86_64/lib/site_perl/5.24.1/x86_64-linux /software/perl-5.24.1-el7-x86_64/lib/site_perl/5.24.1 /software/perl-5.24.1-el7-x86_64/lib/site_perl/5.24.1/x86_64-linux /software/perl-5.24.1-el7-x86_64/lib/site_perl/5.24.1 /software/perl-5.24.1-el7-x86_64/lib/5.24.1/x86_64-linux /software/perl-5.24.1-el7-x86_64/lib/5.24.1 .) at /home/caiqi/CTK_toolkit/ctk/fastq_filter.pl line 10.

I have no idea where is the problem, can anyone help me out at this step?

Thanks,

cAI

BEGIN failed--compilation aborted at /home/caiqi/CTK_toolkit/ctk/fastq_filter.pl line 10.

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