test example failed - Githubissues

yuzhenpeng commented 2 years ago

Hi,

When I run the example, I got the warnings. Could you help me.

`$perl ../DESCHRAMBLER.pl ./params.txt

Constructing syntenic fragments

Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/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 chr2 .. in ref chr1 ......
adding outgroup spc3 in ref chr3 .Cannot open /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/chain/spc1/spc3/chain/chr3.chain. make: *** [Makefile:23: Building.Blocks] Error 1 Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/net
processing spc2.raw.segs
getting segments from spc2.processed.segs
adding descendent spc2 in ref chr3 in ref chr2 .. in ref chr1 ...... Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc3/net
processing spc3.raw.segs
getting segments from spc3.processed.segs
adding descendent spc3 in ref chr3 ... in ref chr2 ..... in ref chr1 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7.

Totally 0 APCFs sh: line 1: 497883 Segmentation fault (core dumped) /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/config.file /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/Ancestor.APCF /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/Conserved.Segments > /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/APCFs`

Thank you.

Morriyaty commented 2 years ago

Have you fixed it? I met a similar error and my log file listed followed. log.txt .

jkimlab commented 2 years ago

Hi,

When I run the example, I got the warnings. Could you help me.

`$perl ../DESCHRAMBLER.pl ./params.txt

Constructing syntenic fragments

Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/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 chr2 .. in ref chr1 ......

adding outgroup spc3 in ref chr3 .Cannot open /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/chain/spc1/spc3/chain/chr3.chain. make: *** [Makefile:23: Building.Blocks] Error 1 Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/net

processing spc2.raw.segs

getting segments from spc2.processed.segs

adding descendent spc2 in ref chr3 in ref chr2 .. in ref chr1 ...... Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc3/net

processing spc3.raw.segs

getting segments from spc3.processed.segs

adding descendent spc3 in ref chr3 ... in ref chr2 ..... in ref chr1 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7.

Totally 0 APCFs sh: line 1: 497883 Segmentation fault (core dumped) /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/config.file /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/Ancestor.APCF /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/Conserved.Segments > /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/APCFs`

Thank you.

Hi,

When I run the example, I got the warnings. Could you help me.

`$perl ../DESCHRAMBLER.pl ./params.txt

Constructing syntenic fragments

Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/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 chr2 .. in ref chr1 ......

adding outgroup spc3 in ref chr3 .Cannot open /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/chain/spc1/spc3/chain/chr3.chain. make: *** [Makefile:23: Building.Blocks] Error 1 Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc2/net

processing spc2.raw.segs

getting segments from spc2.processed.segs

adding descendent spc2 in ref chr3 in ref chr2 .. in ref chr1 ...... Error - Could not open net dir /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/spc1/spc3/net

processing spc3.raw.segs

getting segments from spc3.processed.segs

adding descendent spc3 in ref chr3 ... in ref chr2 ..... in ref chr1 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/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 /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/join_splits.pl line 7.

Totally 0 APCFs sh: line 1: 497883 Segmentation fault (core dumped) /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/config.file /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/Ancestor.APCF /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/SFs/Conserved.Segments > /root/data1/yuzhenpeng2021/biosoft/DESCHRAMBLER/examples/APCFs.300K/APCFs`

Thank you.

It looks like the configuration for the chain/net directory might not be done correctly.

Can you show me the inside of the config.SFs file?

Thanks.

jkimlab commented 2 years ago

Have you fixed it? I met a similar error and my log file listed followed. log.txt .

It may be related with the version of Perl.

Can you try using Perl <= v5.16?

Thanks.

Morriyaty commented 2 years ago

@jkimlab When I used the script with perl v5.16.3, I get the such log. How can I fixed it？ log.txt

jkimlab commented 2 years ago

@jkimlab When I used the script with perl v5.16.3, I get the such log. How can I fixed it？ log.txt

It looks like the "inferAdjProb" program was not properly compiled. Did you see any error messages when you first compiled the program?

Morriyaty commented 2 years ago

This is my log file when I compiled the program again. make.log Could you put the compiled program into a singularity container? haha : )

jkimlab commented 2 years ago

This is my log file when I compiled the program again. make.log Could you put the compiled program into a singularity container? haha : )

It may not be that easy. What OS (and version) are you using? If we don't have a machine with the same OS, it may not be possible to do that.

Morriyaty commented 2 years ago

Is there anything wrong with my make.log file when I compiled the program? I use linux with Centos.

jkimlab commented 2 years ago

Which version?

On Apr 7, 2022, at 3:57 PM, Morriyaty @.***> wrote:

Is there anything wrong with my make.log file when I compiled the program? I use linux with Centos.

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/10#issuecomment-1091147950, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV3NVA2VVI3Y5VCQFWDVD2BOBANCNFSM5SCLS53A. You are receiving this because you were mentioned.

Morriyaty commented 2 years ago

Centos 8.5

jkimlab commented 2 years ago

I can’t make a program including the library because I don’t have a machine with Centos 8.5.

Alternatively, you can try to install the missing library in your machine.

Try to install the GLIBC 2.28 by downloading the file from the following website. If you are not an administrator of the machine, ask the admin. do to that. https://centos.pkgs.org/8/centos-baseos-x86_64/glibc-2.28-164.el8.x86_64.rpm.html https://centos.pkgs.org/8/centos-baseos-x86_64/glibc-2.28-164.el8.x86_64.rpm.html

After that, recompile (type make clean; make) and run again. I hope this helps you.

On Apr 8, 2022, at 5:37 PM, Morriyaty @.***> wrote:

Centos 8.5

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/10#issuecomment-1092604131, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV7RXDUHRM6KKYHPQBLVD7V6PANCNFSM5SCLS53A. You are receiving this because you were mentioned.

jkimlab / DESCHRAMBLER

test example failed #10

Constructing syntenic fragments

Constructing syntenic fragments

Constructing syntenic fragments