test example file failed

[kuangzhuoran]

Hi, Error while running data from example Linux: Centos 8.5
perl v5.32.1

herr is my log log.txt

Or I print it out:

Constructing syntenic fragments

• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
• processing spc2.raw.segs
• processing spc3.raw.segs
• getting segments from spc2.processed.segs
• getting segments from spc3.processed.segs
• adding descendent spc2 in ref chr3 in ref chr1 ...... in ref chr2 ..
• adding outgroup spc3 in ref chr3 ... in ref chr1 ..... in ref chr2 ..... /bin/sh: line 1: 4090473 Segmentation fault (core dumped) /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/code/makeBlocks/createGenomeFile config.file Conserved.Segments > Genomes.Order make: *** [Makefile:57: Genomes.Order] Error 139
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
• processing spc2.raw.segs
• getting segments from spc2.processed.segs
• adding descendent spc2 in ref chr3 in ref chr1 ...... in ref chr2 ..
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
• reading /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
• processing spc3.raw.segs
• getting segments from spc3.processed.segs
• adding descendent spc3 in ref chr3 ... in ref chr1 ..... in ref chr2 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

UNIVERSAL does not export anything at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl5/base.pm line 138. ...propagated at /usr/share/perl5/base.pm line 160. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/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 /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl5/base.pm line 138. ...propagated at /usr/share/perl5/base.pm line 160. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. Compilation failed in require at /usr/share/perl5/base.pm line 138. ...propagated at /usr/share/perl5/base.pm line 160. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/join_splits.pl line 7.

• Totally 0 APCFs sh: line 1: 4090584 Segmentation fault (core dumped) /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/APCFs.300K/SFs/config.file /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/APCFs.300K/Ancestor.APCF /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/APCFs.300K/SFs/Conserved.Segments > /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/examples/APCFs.300K/APCFs

[jkimlab]

Very sorry for my late response.

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.

[kuangzhuoran]

Thanks a lot, It works!