Compilation failed in require at /usr/share/perl5/base.pm line 138.

[hoyosmanuel]

Hello, warm regards. I have been trying to run the program example, but I'm getting an error that I can't understand. I will paste it below. Can you please help me?

## Constructing syntenic fragments ##
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.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 chr1 ......
  in ref chr2 ..
  in ref chr3
- adding outgroup spc3
  in ref chr1 .....
  in ref chr2 .....
  in ref chr3 ...
UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/makeTargetCS.pl line 7.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/makeTargetCS.pl line 7.
make: *** [Makefile:44: Conserved.Segments] Error 255
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
- processing spc2.raw.segs
- getting segments from spc2.processed.segs
- adding descendent spc2
  in ref chr1 ......
  in ref chr2 ..
  in ref chr3
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.net
- processing spc3.raw.segs
- getting segments from spc3.processed.segs
- adding descendent spc3
  in ref chr1 .....
  in ref chr2 .....
  in ref chr3 ...
TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 37.
Use of uninitialized value $tmp in scalar chomp at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 39.
Use of uninitialized value $tmp in substr at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40.
substr outside of string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40.
Use of uninitialized value $numblocks in concatenation (.) or string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 41.
UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 7.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 7.
Estimate JC parameter:
cp: cannot stat 'APCFs.300K/SFs/Genomes.Order': No such file or directory
inferAdjProb - inferring the posterior probability of block adjacency
  usage: inferAdjProb refspc parameter-alpha tree-file genome-file

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/refine_adjprob.pl line 11.
Minimum weight = 0.0001
Conservation score file = APCFs.300K/SFs/block_consscores.txt
UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 7.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 7.
UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 7.
BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 7.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
- Totally 0 APCFs
sh: line 1: 49461 Segmentation fault      (core dumped) /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../code/makeBlocks/createCarFile APCFs.300K/SFs/config.file APCFs.300K/Ancestor.APCF APCFs.300K/SFs/Conserved.Segments > APCFs.300K/APCFs 

[jkimlab]

I think it may be because the BioPerl library in the /lib/perl/ is not compatible with a newer version of Perl.

I attached a new version.

Please completely replace the "Bio" directory in /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.



On May 18, 2023, at 12:07 PM, Manuel Hoyos @.***> wrote:

Hello, warm regards. I have been trying to run the program example, but I'm getting an error that I can't understand. I will paste it below. Can you please help me?

Constructing syntenic fragments

• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.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 chr1 ...... in ref chr2 .. in ref chr3
• adding outgroup spc3 in ref chr1 ..... in ref chr2 ..... in ref chr3 ... UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/makeTargetCS.pl line 7. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/makeTargetCS.pl line 7. make: *** [Makefile:44: Conserved.Segments] Error 255
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
• processing spc2.raw.segs
• getting segments from spc2.processed.segs
• adding descendent spc2 in ref chr1 ...... in ref chr2 .. in ref chr3
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
• reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.net
• processing spc3.raw.segs
• getting segments from spc3.processed.segs
• adding descendent spc3 in ref chr1 ..... in ref chr2 ..... in ref chr3 ... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 37. Use of uninitialized value $tmp in scalar chomp at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 39. Use of uninitialized value $tmp in substr at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40. substr outside of string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40. Use of uninitialized value $numblocks in concatenation (.) or string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 41. UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 7. Estimate JC parameter: cp: cannot stat 'APCFs.300K/SFs/Genomes.Order': No such file or directory inferAdjProb - inferring the posterior probability of block adjacency usage: inferAdjProb refspc parameter-alpha tree-file genome-file

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/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 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 7. readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114. readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114. readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.

• Totally 0 APCFs sh: line 1: 49461 Segmentation fault (core dumped) /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../code/makeBlocks/createCarFile APCFs.300K/SFs/config.file APCFs.300K/Ancestor.APCF APCFs.300K/SFs/Conserved.Segments > APCFs.300K/APCFs — Reply to this email directly, view it on GitHub https://github.com/ma-compbio/DESCHRAMBLER/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV2HBO3UVS5LHEFLV3DXGWHAJANCNFSM6AAAAAAYF4XYJE. You are receiving this because you are subscribed to this thread.

[hoyosmanuel]

Dear OBJ, thank you very much for your response. Could you please clarify where the new version of the file you mentioned is attached? Thank you so much, and I'll be waiting for your reply.

[jkimlab]

I emailed the file, and I think it didn’t work.

You can find the file in the following similar issue.

https://github.com/jkimlab/DESCHRAMBLER/issues/11

On May 18, 2023, at 11:48 PM, Manuel Hoyos @.***> wrote:

Dear OBJ, thank you very much for your response. Could you please clarify where the new version of the file you mentioned is attached? Thank you so much, and I'll be waiting for your reply.

— Reply to this email directly, view it on GitHub https://github.com/ma-compbio/DESCHRAMBLER/issues/2#issuecomment-1553177908, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV4CW2IFGM3EDCTV6H3XGYZEBANCNFSM6AAAAAAYF4XYJE. You are receiving this because you commented.

[hoyosmanuel]

Thank you OBJ, I used the new Bio.tar.gz file you mentioned and now I received this error:

## Constructing syntenic fragments ##
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.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 chr1 ......
  in ref chr2 ..
  in ref chr3
- adding outgroup spc3
  in ref chr1 .....
  in ref chr2 .....
  in ref chr3 ...
/bin/sh: line 1: 49716 Segmentation fault      (core dumped) /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/orthoBlocksToOrders config.file _orthology.blocks.tmp > _order.DS
make: *** [Makefile:39: Conserved.Segments] Error 139
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/create_blocklist.pl line 18.
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc2/net/chr3.net
- processing spc2.raw.segs
- getting segments from spc2.processed.segs
- adding descendent spc2
  in ref chr1 ......
  in ref chr2 ..
  in ref chr3
/bin/sh: line 1: 49752 Segmentation fault      (core dumped) /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/orthoBlocksToOrders config.file _orthology.blocks.tmp > _order.DS
make: *** [Makefile:48: Conserved.Segments.pair] Error 139
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estimate_bpdist4.pl line 61.
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr1.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr2.net
- reading /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/chainNet/spc1/spc3/net/chr3.net
- processing spc3.raw.segs
- getting segments from spc3.processed.segs
- adding descendent spc3
  in ref chr1 .....
  in ref chr2 .....
  in ref chr3 ...
/bin/sh: line 1: 49786 Segmentation fault      (core dumped) /lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/orthoBlocksToOrders config.file _orthology.blocks.tmp > _order.DS
make: *** [Makefile:48: Conserved.Segments.pair] Error 139
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estimate_bpdist4.pl line 61.
TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 37.
Use of uninitialized value $tmp in scalar chomp at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 39.
Use of uninitialized value $tmp in substr at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40.
substr outside of string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 40.
Use of uninitialized value $numblocks in concatenation (.) or string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 41.
Use of uninitialized value $bdist_f in concatenation (.) or string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 14.
spc1 /lustre/work/mhoyosro/software/DESCHRAMBLER-master/examples/tree.txt APCFs.300K/SFs/bpdist.txt
Use of uninitialized value $bdist_f in string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 17.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/estparJC.pl line 18.
Estimate JC parameter: 0.0001
cp: cannot stat 'APCFs.300K/SFs/Genomes.Order': No such file or directory
Can't exec "/lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../code/inferAdjProb": No such file or directory at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 52.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/refine_adjprob.pl line 11.
Can't exec "/lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../code/deschrambler": No such file or directory at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/wrap_recon_apcf.pl line 59.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/add_missing_blocks.pl line 22.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 130.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 130.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/split_weak_joins.pl line 130.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 60.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 131.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 131.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 131.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 156.
Use of uninitialized value $join_header in scalar chomp at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 188.
Use of uninitialized value $join_header in concatenation (.) or string at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/join_splits.pl line 295.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/sort_apcfs.pl line 13.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/ext_join_info.pl line 114.
sh: /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/../code/makeBlocks/createCarFile: No such file or directory
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/create_mapfile.pl line 42.
readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/script/create_mapfile.pl line 64.

Any idea?

[jkimlab]

I think the parameter file was not set correctly. Can you show me the content of the parameter file and the command line?

One more thing. If it is possible, please open a new issue in the following GitHub site.

https://github.com/jkimlab/DESCHRAMBLER

On May 19, 2023, at 4:39 AM, Manuel Hoyos @.***> wrote:

Thank you OBJ, I used the new Bio.tar.gz file you mentioned and now I received this error:

readline() on closed filehandle F at /lustre/work/mhoyosro/software/DESCHRAMBLER-master/DESCHRAMBLER.pl line 20. missing parameters: REFSPC OUTPUTDIR RESOLUTION TREEFILE CONFIGSFSFILE MAKESFSFILE MINADJSCR Any idea?

— Reply to this email directly, view it on GitHub https://github.com/ma-compbio/DESCHRAMBLER/issues/2#issuecomment-1553554834, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV3RE5YKPIJYPDM2BRLXGZ3HJANCNFSM6AAAAAAYF4XYJE. You are receiving this because you commented.

[hoyosmanuel]

Done. Thank you OBJ.