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Does not export anything at <DESCHRAMBLER-path>/TreeFunctionsI.pm line 94. #12

Closed goblin290272908 closed 1 year ago

goblin290272908 commented 1 year ago

Hi, Thank you for providing such an excellent tool. But, when I run the example, I got the Err . Could you help me?

Linux: ubuntu 20.04 perl: v5.26.2 and 5.30.0 GLIBC: 2.31

I print it out:

Constructing syntenic fragments

UNIVERSAL does not export anything at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. ...propagated at /usr/share/perl/5.30/base.pm line 159. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/estparJC.pl line 7. Estimate JC parameter: inferAdjProb - inferring the posterior probability of block adjacency usage: inferAdjProb refspc parameter-alpha tree-file genome-file

readline() on closed filehandle F at /home/manager/bioapps/DESCHRAMBLER-master/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /home/manager/bioapps/DESCHRAMBLER-master/examples/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. ...propagated at /usr/share/perl/5.30/base.pm line 159. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl/5.30/base.pm line 137. ...propagated at /usr/share/perl/5.30/base.pm line 159. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/manager/bioapps/DESCHRAMBLER-master/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /home/manager/bioapps/DESCHRAMBLER-master/script/join_splits.pl line 7.

thankyou!!!!!!!!!

jkimlab commented 1 year ago

I think it is because the BioPerl library in the \<path to DESCHRAMBLER>/lib/perl/ is not compatible with a newer version of Perl.

I attached a new version. Bio.tar.gz

Please completely replace the "Bio" directory in \<path to DESCHRAMBLER>/lib/perl/ by the attached one after uncompressing and untarring it.

After that, you can rerun DESCHRAMBLER. Please don't forget to delete the previously created output directory.

Thanks.

goblin290272908 commented 1 year ago

Thank you for your prompt response. My perllib path is /home/manager/perl5/lib/perl5/Bio, and i replace it with your DIR. i find my perllib use command “$ perldoc -l Bio::Seq”。 However, it still prompts the previous error.

jkimlab commented 1 year ago

Sorry. My previous response was not entered correctly.

DESCRAMBLER is hard-coded to use the BioPerl library in the "lib/perl/" subdirectory in the install directory of DESCRAMBLER. Therefore, you have to replace the "Bio" subdirectory there, not in /home/manager/perl5/lib/perl5/.

goblin290272908 commented 1 year ago

Thank you very much!!!!!!! all done !!!! Ammmmazing！