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Segmentation fault (core dumped) #13

Closed hoyosmanuel closed 1 year ago

hoyosmanuel commented 1 year ago

Hi, kind regards. I received an error while running the example. As a background, I mention that I am using an updated version of the "Bio" directory obtained from here: https://github.com/jkimlab/DESCHRAMBLER/issues/11. I am also attaching my params.txt file. Can you please help me?

This is my "params.txt" file

# Reference species
REFSPC=spc1

# Output directory
OUTPUTDIR=APCFs.300K
#OUTPUTDIR=Out_RACA.anctest

# Block resolution (bp)
RESOLUTION=300000

# Newick tree file
# Refer to the sample file 'tree.txt'.
TREEFILE=tree.txt

# Minimum adjacency scores
MINADJSCR=0.0001

# Config and make files for syntenic fragment construction
# Refer to the sample files 'config.SFs' and 'Makefile.SFs'.
# You need to change settings in the sample configuration file (config.SFs) according to your data
# You don't need to change anything in the Makefile.SFs.
CONFIGSFSFILE=config.SFs
MAKESFSFILE=Makefile.SFs

This is the error I've obtained

## 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: 123098 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: 123131 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: 123163 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.
jkimlab commented 1 year ago

Did you see any error message when making the program? It looks like the synteny generation program didn’t run correctly.

On May 19, 2023, at 11:51 AM, Manuel Hoyos @.***> wrote:

Hi, kind regards. I received an error while running the example. As a background, I mention that I am using an updated version of the "Bio" directory obtained from here: #11 https://github.com/jkimlab/DESCHRAMBLER/issues/11. I am also attaching my params.txt file. Can you please help me?

This is my "params.txt" file

Reference species

REFSPC=spc1

Output directory

OUTPUTDIR=APCFs.300K

OUTPUTDIR=Out_RACA.anctest

Block resolution (bp)

RESOLUTION=300000

Newick tree file

Refer to the sample file 'tree.txt'.

TREEFILE=tree.txt

Minimum adjacency scores

MINADJSCR=0.0001

Config and make files for syntenic fragment construction

Refer to the sample files 'config.SFs' and 'Makefile.SFs'.

You need to change settings in the sample configuration file (config.SFs) according to your data

You don't need to change anything in the Makefile.SFs.

CONFIGSFSFILE=config.SFs MAKESFSFILE=Makefile.SFs This is the error I've obtained

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: 123098 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: 123131 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: 123163 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. — Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/13, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV2BDJRUJDY6U4NPXWTXG3N3ZANCNFSM6AAAAAAYHGZC3E. You are receiving this because you are subscribed to this thread.

hoyosmanuel commented 1 year ago

Yes, during the final phase of installation, I encountered this error that I cannot fix:

 sprintf(netfile, "%s/%s/%s/net/%s.net", 

    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

         Netdir, Spename[0], Spename[ss], refchrom); 

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. getSegments.c util.o species.o -o getSegments 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. partitionGenomes.c util.o base.o species.o -o partitionGenomes 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. makeOrthologyBlocks.c util.o species.o -o makeOrthologyBlocks 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. makeOrthologyBlocks.pair.c util.o species.o -o makeOrthologyBlocks.pair 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. orthoBlocksToOrders.c util.o species.o -o orthoBlocksToOrders 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. makeConservedSegments.c util.o species.o -o makeConservedSegments 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. outgroupSegsToOrders.c util.o species.o -o outgroupSegsToOrders 

gcc -ggdb -g -mcmodel=medium -W -Wall -I. cleanOutgroupSegs.c util.o species.o -o cleanOutgroupSegs 

/tmp/ccPBwaTb.o: In function `remove_tiny_pieces': 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:68:(.text+0x284): relocation truncated to fit: R_X86_64_32S against symbol `Spetag' defined in COMMON section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:67:(.text+0x3a9): relocation truncated to fit: R_X86_64_PC32 against symbol `Spesz' defined in .bss section in species.o 

/tmp/ccPBwaTb.o: In function `main': 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:116:(.text+0x46d): relocation truncated to fit: R_X86_64_32S against symbol `Spetag' defined in COMMON section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:115:(.text+0x518): relocation truncated to fit: R_X86_64_PC32 against symbol `Spesz' defined in .bss section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:149:(.text+0x715): relocation truncated to fit: R_X86_64_32S against symbol `Spetag' defined in COMMON section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:148:(.text+0x979): relocation truncated to fit: R_X86_64_PC32 against symbol `Spesz' defined in .bss section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:182:(.text+0xa4e): relocation truncated to fit: R_X86_64_32S against symbol `Spename' defined in .bss section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:183:(.text+0xa7e): relocation truncated to fit: R_X86_64_32S against symbol `Spetag' defined in COMMON section in species.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/cleanOutgroupSegs.c:179:(.text+0xb12): relocation truncated to fit: R_X86_64_PC32 against symbol `Spesz' defined in .bss section in species.o 

util.o: In function `print_argv0': 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/util.c:12:(.text+0xb): relocation truncated to fit: R_X86_64_PC32 against symbol `argv0' defined in COMMON section in util.o 

/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks/util.c:13:(.text+0x17): additional relocation overflows omitted from the output 

collect2: error: ld returned 1 exit status 

make[1]: *** [Makefile:29: cleanOutgroupSegs] Error 1 

make[1]: Leaving directory '/lustre/work/mhoyosro/software/DESCHRAMBLER-master/code/makeBlocks' 

make: *** [Makefile:6: all] Error 2
hoyosmanuel commented 1 year ago

I found a solution. A colleague of mine who has experience with this program warned me that its functionality depends on the cluster where it is run. In my case, I changed the partition (from "nocona" to "quanah"), replaced the "Bio" folder within the "lib" directory, re-installed the program, and ran the example. I didn't encounter any errors. Regards.

jkimlab commented 1 year ago

Good to hear that! Thanks.

On May 20, 2023, at 2:02 AM, Manuel Hoyos @.***> wrote:

I found a solution. A colleague of mine who has experience with this program warned me that its functionality depends on the cluster where it is run. In my case, I changed the partition (from "nocona" to "quanah"), replaced the "Bio" folder within the "lib" directory, re-installed the program, and ran the example. I didn't encounter any errors. Regards.

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/13#issuecomment-1554937608, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PVYJ3K3LUNRETURYJ73XG6RTPANCNFSM6AAAAAAYHGZC3E. You are receiving this because you commented.