Fix code to run DESCHRAMBLER on example dir by Dhananjhay · Pull Request #33 · jkimlab/DESCHRAMBLER

Dhananjhay · 2025-09-19T06:51:55Z

This PR patches the code to stop explicitly using use UNIVERSAL qw(isa) as it's a deprecated practice and causes the tool to fail when working with the example dir shipped with the package.

Command I was running:

(base) dbansal7@UWO-CBS-Heavy23:/localscratch/DESCHRAMBLER/examples$ perl ../DESCHRAMBLER.pl params.txt

Error log:

## Constructing syntenic fragments ##
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 135.
	...propagated at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 157.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/code/makeBlocks/../../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /local/scratch/DESCHRAMBLER/code/makeBlocks/makeTargetCS.pl line 7.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/code/makeBlocks/makeTargetCS.pl line 7.
make: *** [Makefile:44: Conserved.Segments] Error 255
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/script/wrap_recon_apcf.pl line 37.
Use of uninitialized value $tmp in scalar chomp at /local/scratch/DESCHRAMBLER/script/wrap_recon_apcf.pl line 39.
Use of uninitialized value $tmp in substr at /local/scratch/DESCHRAMBLER/script/wrap_recon_apcf.pl line 40.
substr outside of string at /local/scratch/DESCHRAMBLER/script/wrap_recon_apcf.pl line 40.
Use of uninitialized value $numblocks in concatenation (.) or string at /local/scratch/DESCHRAMBLER/script/wrap_recon_apcf.pl line 41.
UNIVERSAL does not export anything at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 135.
	...propagated at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 157.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/estparJC.pl line 7.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 135.
	...propagated at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 157.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/split_weak_joins.pl line 7.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/split_weak_joins.pl line 7.
UNIVERSAL does not export anything at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94.
Compilation failed in require at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 135.
	...propagated at /usr/lib/x86_64-linux-gnu/perl-base/base.pm line 157.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90.
Compilation failed in require at /local/scratch/DESCHRAMBLER/script/join_splits.pl line 7.
BEGIN failed--compilation aborted at /local/scratch/DESCHRAMBLER/script/join_splits.pl line 7.
readline() on closed filehandle F at /local/scratch/DESCHRAMBLER/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /local/scratch/DESCHRAMBLER/script/ext_join_info.pl line 114.
readline() on closed filehandle F at /local/scratch/DESCHRAMBLER/script/ext_join_info.pl line 114.
- Totally 0 APCFs
Segmentation fault (core dumped)

After commenting out use UNIVERSAL qw(isa), output I get:

## Constructing syntenic fragments ##
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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 ...
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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 /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
- reading /local/scratch/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
- reading /local/scratch/DESCHRAMBLER/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);

24 spc1 /local/scratch/DESCHRAMBLER/examples/tree.txt APCFs.300K/SFs/bpdist.txt
Estimate JC parameter: 0.880232496468603
readLeafGenomes: spc1
readLeafGenomes: spc2
T=24
Initializing spc1 (ingroup)
Initializing spc2 (ingroup)
Initializing spc3 (outgroup)
Computing posterior probabilities ...
Minimum weight = 0.0001
Conservation score file = APCFs.300K/SFs/block_consscores.txt
- Totally 9 APCFs

no need for explicit import ofusf use UNUNIVERSAL qw(isa)

5e1020c

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Fix code to run DESCHRAMBLER on example dir#33

Fix code to run DESCHRAMBLER on example dir#33
Dhananjhay wants to merge 1 commit intojkimlab:masterfrom
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Dhananjhay commented Sep 19, 2025

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Dhananjhay commented Sep 19, 2025

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