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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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perl errors while running JUM_B #43

Open dzijlmans opened 1 year ago

dzijlmans commented 1 year ago

Hi,

When executing the JUM_B.sh script, I kept getting the following errors

(base) dzijlmans@cn45:/scratch/dzijlmans/DZ046/JUM_single/Ctrl_vs_dTAG_4h/JUM_diff$ bash /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/JUM_B.sh --Folder /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2 --Test pvalue --Cutoff 0.05 --TotalFileNum 8 --Condition1_fileNum_threshold 3 --Condition2_fileNum_threshold 3 --Condition1SampleName Ctrl_rep1,Ctrl_rep2,Ctrl_rep3,Ctrl_rep4 --Condition2SampleName dTAG_4h_rep1,dTAG_4h_rep2,dTAG_4h_rep3,dTAG_4h_rep4
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `dTAG_4h_rep2_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep3_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `dTAG_4h_rep3_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep1_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
awk: fatal: cannot open file `Ctrl_rep4_long_intron_retention_screening_pvalue_0.05.txt' for reading (No such file or directory)
Can't locate Statistics/Descriptive.pm in @INC (you may need to install the Statistics::Descriptive module) (@INC contains: /vol/mbconda/dzijlmans/lib/perl5/5.32/site_perl /vol/mbconda/dzijlmans/lib/perl5/site_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/vendor_perl /vol/mbconda/dzijlmans/lib/perl5/5.32/core_perl /vol/mbconda/dzijlmans/lib/perl5/core_perl .) at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.
BEGIN failed--compilation aborted at /scratch/dzijlmans/DZ046/JUM_single/JUM_2.0.2/determining_rightful_long_intron_retention_event_updated.pl line 4.

and so on, similar to #7. While the script completed running, the output files were mostly empty, containing only headers and no AS sites.

It turned out the Statistics::Descriptive and Array::Utils modules were not installed and I had to install them manually using

mamba install perl-app-cpanminus cpanm Statistics::Descriptive cpanm Array::Utils

After installing these modules, the script ran with no further issues and generated output files containing AS events Would it be possible for you to add the installation of these packages to the JUM_C script for future users?

Best, Dick

qqwang-berkeley commented 1 year ago

Yes this error was caused by not installed the corresponding modules on user end. Please see the manual on "installation": Requirements: Perl (5+) with modules Array::Utils and Statistics::Descriptive (for checking if modules are already installed and instructions of installing perl modules see Additional Installation Tips below)