Trouble with handling the test run

[Alchimic007]

Hello,

Could you help me with this complex issue while running DESCHRAMBLER for test example files. server hpc cluster qsub I would be very appreciated for any help.

here is error messages:

Constructing syntenic fragments

/users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10:int get_level (char *s) {' make: * [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/create_blocklist.pl line 18. /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10:int get_level (char s) {' make: [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/estimate_bpdist4.pl line 61. /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10:int get_level (char *s) {' make: *** [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/estimate_bpdist4.pl line 61. TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

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

[jkimlab]

Hello,

Did you compile the code successfully in hpc? We couldn’t test the code in hpc.

On Oct 3, 2023, at 11:54 PM, Alchimic007 @.***> wrote:

Hello,

Could you help me with this complex issue while running DESCHRAMBLER for test example files. server hpc cluster qsub I would be very appreciated for nay help.

here is error messages:

Constructing syntenic fragments

/users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: int get_level (char *s) {' make: * [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/create_blocklist.pl line 18. /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: int get_level (char s) {' make: [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/estimate_bpdist4.pl line 61. /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: syntax error near unexpected token (' /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks/readNets: line 10: int get_level (char *s) {' make: *** [Grab.Data] Error 2 readline() on closed filehandle F at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/estimate_bpdist4.pl line 61. TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

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

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[Alchimic007]

Hello,

Sorry to disturb you again. Yes, you were right previous errors appeared because I hadn't compiled files correctly, but now I managed to solve this on hpc cluster. Here is log [hpctestuser@login1(rvchpc1) ~]$ cd /users/hpctestuser/mprylutskyi/DESCHRAMBLER [hpctestuser@login1(rvchpc1) DESCHRAMBLER]$ make sed -e 's::/users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/chainNet:g' examples/config.SFs.tmp > examples/config.SFs cd lib/kent/src/lib && make make[1]: Entering directory /users/hpctestuser/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib' gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o verbose.o -c verbose.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errabort.o -c errabort.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dystring.o -c dystring.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o common.o -c common.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dlist.o -c dlist.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o wildcmp.o -c wildcmp.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o options.o -c options.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o osunix.o -c osunix.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o obscure.o -c obscure.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pipeline.o -c pipeline.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memalloc.o -c memalloc.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o linefile.o -c linefile.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o localmem.o -c localmem.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hash.o -c hash.c ar rcus jkweb.a verbose.o errabort.o dystring.o common.o dlist.o wildcmp.o options.o osunix.o obscure.o pipeline.o memalloc.o linefile.o localmem.o hash.o make[1]: Leaving directory/users/hpctestuser/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib' cd code/makeBlocks && make make[1]: Entering directory /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks' gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c util.c gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c base.c gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c species.c gcc -ggdb -g -mcmodel=medium -W -Wall -I. checkNets.c util.o species.o -o checkNets gcc -ggdb -g -mcmodel=medium -W -Wall -I. readNets.c util.o species.o -o readNets 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 gcc -ggdb -g -mcmodel=medium -W -Wall -I. createGenomeFile.c util.o species.o -o createGenomeFile gcc -ggdb -g -mcmodel=medium -W -Wall -I. createCarFile.c util.o species.o -o createCarFile gcc -ggdb -g -mcmodel=medium -W -Wall -I. splitChain.c util.o species.o -o splitChain gcc -ggdb -g -mcmodel=medium -W -Wall -I. splitNet.c util.o species.o -o splitNet gcc -ggdb -g -mcmodel=medium -W -Wall -I. onlySpe.c util.o species.o -o onlySpe gcc -ggdb -g -mcmodel=medium -W -Wall -I. bpPosition.c util.o species.o -o bpPosition gcc -ggdb -g -mcmodel=medium -W -Wall -I. mergePieces.c util.o species.o -o mergePieces make[1]: Leaving directory/users/hpctestuser/mprylutskyi/DESCHRAMBLER/code/makeBlocks' cd code && make make[1]: Entering directory /users/hpctestuser/mprylutskyi/DESCHRAMBLER/code' gcc -g -W -O3 -I. -I../lib/kent/src/inc inferAdjProb.c ../lib/kent/src/lib//jkweb.a -lm -o inferAdjProb g++ deschrambler.cpp -o deschrambler make[1]: Leaving directory/users/hpctestuser/mprylutskyi/DESCHRAMBLER/code'

[Alchimic007]

But, I have another issue when running DESCHRAMBLER with example files. Here it is. ## Constructing syntenic fragments ## sed: can't read config.SFs: No such file or directory sed: can't read Makefile.SFs: No such file or directory make: *** No rule to make target `all'. Stop. Can't exec "/users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/create_blocklist.pl": Permission denied at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 51. Can't exec "/users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/wrap_recon_apcf.pl": Permission denied at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 54.

[Alchimic007]

this happens if do not change anything in config or params file

[Alchimic007]

And this is what happen if I specify path to config,sf, make.sf and tree.txt files

Constructing syntenic fragments

cannot parse species

make: *** [Grab.Data] Error 1 Can't exec "/users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/create_blocklist.pl": Permission denied at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 51. Can't exec "/users/hpctestuser/mprylutskyi/DESCHRAMBLER/script/wrap_recon_apcf.pl": Permission denied at /users/hpctestuser/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 54. [hpctestuser@login1(rvchpc1) DESCHRAMBLER]$

[Alchimic007]

here are my config file

path of a net files

netdir /users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/chainNet

path of a chain files

chaindir /users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/chainNet

species-name tag1 tag2

tag1 (0: ref-species, 1: descendents, 2: outgroup)

tag2 (1: chromosome assembly, 0: others)

Warning for tag2: Use the value 1 only when a chromosome name starts with "chr".

species spc1 0 1 spc2 1 1 spc3 2 1

block resolution (bp): DO NOT CHANGE

resolution

[Alchimic007]

and 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=/users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/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=/users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/config.SFs MAKESFSFILE=/users/hpctestuser/mprylutskyi/DESCHRAMBLER/examples/Makefile.SFs

[Alchimic007]

I have also tried to compile it on SLURM cluster but got fail messages

mprylutskyi@cm-hpc-login01:~> cd /storage/users/mprylutskyi/DESCHRAMBLER mprylutskyi@cm-hpc-login01:~/DESCHRAMBLER> make sed -e 's::/storage/users/mprylutskyi/DESCHRAMBLER/examples/chainNet:g' examples/config.SFs.tmp > examples/config.SFs cd lib/kent/src/lib && make make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib' gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o verbose.o -c verbose.c verbose.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: verbose.c,v 1.7 2010/04/01 17:31:10 markd Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errabort.o -c errabort.c errabort.c:28:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dystring.o -c dystring.c dystring.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: dystring.c,v 1.25 2009/11/13 19:01:56 kent Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o common.o -c common.c common.c:13:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: common.c,v 1.151 2010/06/02 19:06:41 tdreszer Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dlist.o -c dlist.c dlist.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: dlist.c,v 1.11 2005/07/04 18:44:09 markd Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o wildcmp.o -c wildcmp.c wildcmp.c:8:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: wildcmp.c,v 1.7 2009/11/20 19:11:16 angie Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o options.o -c options.c options.c: In function ‘validateOption’: options.c:53:11: warning: variable ‘discardMe’ set but not used [-Wunused-but-set-variable] long long discardMe = 0; ^~~~~ At top level: options.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: options.c,v 1.29 2009/12/02 19:10:38 kent Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o osunix.o -c osunix.c osunix.c:19:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: osunix.c,v 1.48 2010/06/03 05:14:39 kent Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o obscure.o -c obscure.c obscure.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: obscure.c,v 1.53 2010/01/27 21:04:04 galt Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pipeline.o -c pipeline.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memalloc.o -c memalloc.c memalloc.c:16:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: memalloc.c,v 1.31 2007/04/24 18:35:43 hiram Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o linefile.o -c linefile.c gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o localmem.o -c localmem.c localmem.c:14:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: localmem.c,v 1.13 2009/12/03 20:04:29 kent Exp $"; ^~~~~ gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DUSE_SSL -DCOLOR32 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hash.o -c hash.c hash.c:12:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static char const rcsid[] = "$Id: hash.c,v 1.51 2009/11/10 22:46:19 angie Exp $"; ^~~~~ ar rcus jkweb.a verbose.o errabort.o dystring.o common.o dlist.o wildcmp.o options.o osunix.o obscure.o pipeline.o memalloc.o linefile.o localmem.o hash.o make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib' cd code/makeBlocks && make make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks' gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c util.c util.c:1:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] static const char rcsid[]= ^~~~~ gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c base.c gcc -ggdb -g -mcmodel=medium -W -Wall -I. -c species.c gcc -ggdb -g -mcmodel=medium -W -Wall -I. checkNets.c util.o species.o -o checkNets checkNets.c: In function ‘main’: checkNets.c:97:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (sscanf(buf, "%s %d %d %s %c %d %d id %d %s", ^~ checkNets.c:100:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ val[level] = 1; ^~~ gcc -ggdb -g -mcmodel=medium -W -Wall -I. readNets.c util.o species.o -o readNets 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 gcc -ggdb -g -mcmodel=medium -W -Wall -I. createGenomeFile.c util.o species.o -o createGenomeFile gcc -ggdb -g -mcmodel=medium -W -Wall -I. createCarFile.c util.o species.o -o createCarFile gcc -ggdb -g -mcmodel=medium -W -Wall -I. splitChain.c util.o species.o -o splitChain gcc -ggdb -g -mcmodel=medium -W -Wall -I. splitNet.c util.o species.o -o splitNet gcc -ggdb -g -mcmodel=medium -W -Wall -I. onlySpe.c util.o species.o -o onlySpe gcc -ggdb -g -mcmodel=medium -W -Wall -I. bpPosition.c util.o species.o -o bpPosition gcc -ggdb -g -mcmodel=medium -W -Wall -I. mergePieces.c util.o species.o -o mergePieces make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks' cd code && make make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code' gcc -g -W -O3 -I. -I../lib/kent/src/inc inferAdjProb.c ../lib/kent/src/lib//jkweb.a -lm -o inferAdjProb In file included from inferAdjProb.c:5:0: inferAdjProb.c: In function ‘getLP’: uthash.h:424:21: warning: this statement may fall through [-Wimplicit-fallthrough=] case 11: hashv += ( (unsigned)_hj_key[10] << 24 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:425:6: note: here case 10: hashv += ( (unsigned)_hj_key[9] << 16 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:425:21: warning: this statement may fall through [-Wimplicit-fallthrough=] case 10: hashv += ( (unsigned)_hj_key[9] << 16 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:426:6: note: here case 9: hashv += ( (unsigned)_hj_key[8] << 8 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:426:21: warning: this statement may fall through [-Wimplicit-fallthrough=] case 9: hashv += ( (unsigned)_hj_key[8] << 8 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:427:6: note: here case 8: _hj_j += ( (unsigned)_hj_key[7] << 24 ); \ ^ uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’

define HASH_FCN HASH_JEN

              ^~~~~~~~

uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’ HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt); \ ^~~~ inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’ HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry); ^~~~~ uthash.h:427:21: warning: this statement may fall through [-Wimplicit-fallthrough=] case 8: _hj_j += ( (unsigned)_hj_key[7] << 24 ); \

uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:428:6: note: here
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:428:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:429:6: note: here
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:429:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:430:6: note: here
      case 5:  _hj_j += _hj_key[4];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:430:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 5:  _hj_j += _hj_key[4];                                               \
               ~~~~~~^~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:431:6: note: here
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:431:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:432:6: note: here
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:432:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:433:6: note: here
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:433:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:434:6: note: here
      case 1:  _hj_i += _hj_key[0];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:635:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, lp_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:424:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 11: hashv += ( (unsigned)_hj_key[10] << 24 );                          \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:425:6: note: here
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:425:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:426:6: note: here
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:426:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:427:6: note: here
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:427:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:428:6: note: here
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:428:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:429:6: note: here
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:429:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:430:6: note: here
      case 5:  _hj_j += _hj_key[4];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:430:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 5:  _hj_j += _hj_key[4];                                               \
               ~~~~~~^~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:431:6: note: here
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:431:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:432:6: note: here
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:432:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:433:6: note: here
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:433:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:434:6: note: here
      case 1:  _hj_i += _hj_key[0];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:645:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, lp_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
inferAdjProb.c: In function ‘getLL’:
uthash.h:424:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 11: hashv += ( (unsigned)_hj_key[10] << 24 );                          \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:425:6: note: here
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:425:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:426:6: note: here
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:426:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:427:6: note: here
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:427:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:428:6: note: here
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:428:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:429:6: note: here
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:429:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:430:6: note: here
      case 5:  _hj_j += _hj_key[4];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:430:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 5:  _hj_j += _hj_key[4];                                               \
               ~~~~~~^~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:431:6: note: here
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:431:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:432:6: note: here
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:432:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:433:6: note: here
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:433:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:434:6: note: here
      case 1:  _hj_i += _hj_key[0];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:99:6: note: in expansion of macro ‘HASH_FCN’
      HASH_FCN(keyptr,keylen, (head)->hh.tbl->num_buckets, _hf_hashv, _hf_bkt);   \
      ^~~~~~~~
inferAdjProb.c:662:5: note: in expansion of macro ‘HASH_FIND’
     HASH_FIND(hh, ll_cache, &hkey, sizeof(struct hash_key), hentry);
     ^~~~~~~~~
uthash.h:424:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 11: hashv += ( (unsigned)_hj_key[10] << 24 );                          \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:425:6: note: here
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:425:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 10: hashv += ( (unsigned)_hj_key[9] << 16 );                           \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:426:6: note: here
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:426:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 9:  hashv += ( (unsigned)_hj_key[8] << 8 );                            \
                     ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:427:6: note: here
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:427:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 8:  _hj_j += ( (unsigned)_hj_key[7] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:428:6: note: here
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:428:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 7:  _hj_j += ( (unsigned)_hj_key[6] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:429:6: note: here
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:429:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 6:  _hj_j += ( (unsigned)_hj_key[5] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:430:6: note: here
      case 5:  _hj_j += _hj_key[4];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:430:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 5:  _hj_j += _hj_key[4];                                               \
               ~~~~~~^~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:431:6: note: here
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:431:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 4:  _hj_i += ( (unsigned)_hj_key[3] << 24 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:432:6: note: here
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:432:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 3:  _hj_i += ( (unsigned)_hj_key[2] << 16 );                           \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:433:6: note: here
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:433:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
      case 2:  _hj_i += ( (unsigned)_hj_key[1] << 8 );                            \
               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
uthash.h:434:6: note: here
      case 1:  _hj_i += _hj_key[0];                                               \
      ^
uthash.h:334:18: note: in expansion of macro ‘HASH_JEN’
 #define HASH_FCN HASH_JEN
                  ^~~~~~~~
uthash.h:179:2: note: in expansion of macro ‘HASH_FCN’
  HASH_FCN(keyptr,keylen_in, (head)->hh.tbl->num_buckets,                         \
  ^~~~~~~~
uthash.h:160:9: note: in expansion of macro ‘HASH_ADD_KEYPTR’
         HASH_ADD_KEYPTR(hh,head,&((add)->fieldname),keylen_in,add)
         ^~~~~~~~~~~~~~~
inferAdjProb.c:672:9: note: in expansion of macro ‘HASH_ADD’
         HASH_ADD(hh, ll_cache, key, sizeof(struct hash_key), newentry);
         ^~~~~~~~
g++ deschrambler.cpp -o deschrambler
make[1]: g++: Command not found
make[1]: *** [Makefile:21: deschrambler] Error 127
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code'
make: *** [Makefile:7: all] Error 2
mprylutskyi@cm-hpc-login01:~/DESCHRAMBLER> make
sed -e 's:<pathtochainNet>:/storage/users/mprylutskyi/DESCHRAMBLER/examples/chainNet:g' examples/config.SFs.tmp > examples/config.SFs
cd lib/kent/src/lib && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib'
make[1]: 'jkweb.a' is up to date.
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib'
cd code/makeBlocks && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks'
cd code && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code'
g++ deschrambler.cpp -o deschrambler
make[1]: g++: Command not found
make[1]: *** [Makefile:21: deschrambler] Error 127
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code'
make: *** [Makefile:7: all] Error 2
mprylutskyi@cm-hpc-login01:~/DESCHRAMBLER> conda activate condaenv
(condaenv) mprylutskyi@cm-hpc-login01:~/DESCHRAMBLER> make
sed -e 's:<pathtochainNet>:/storage/users/mprylutskyi/DESCHRAMBLER/examples/chainNet:g' examples/config.SFs.tmp > examples/config.SFs
cd lib/kent/src/lib && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib'
make[1]: 'jkweb.a' is up to date.
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/lib/kent/src/lib'
cd code/makeBlocks && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code/makeBlocks'
cd code && make
make[1]: Entering directory '/storage/users/mprylutskyi/DESCHRAMBLER/code'
g++ deschrambler.cpp -o deschrambler
make[1]: g++: Command not found
make[1]: *** [Makefile:21: deschrambler] Error 127
make[1]: Leaving directory '/storage/users/mprylutskyi/DESCHRAMBLER/code'
make: *** [Makefile:7: all] Error 2

[Alchimic007]

it seem same as in hpc cluster

Constructing syntenic fragments

sed: can't read config.SFs: No such file or directory sed: can't read Makefile.SFs: No such file or directory make: *** No rule to make target 'all'. Stop. Can't exec "/storage/users/mprylutskyi/DESCHRAMBLER/script/create_blocklist.pl": Permission denied at /storage/users/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 51. Can't exec "/storage/users/mprylutskyi/DESCHRAMBLER/script/wrap_recon_apcf.pl": Permission denied at /storage/users/mprylutskyi/DESCHRAMBLER/DESCHRAMBLER.pl line 54.

[Alchimic007]

would be grateful for any help

[Alchimic007]

About server specifications : Alces Software HPC Stack For Linux Based on Scientific Linux 6.5 Perl: perl/5.14.2/gcc-4.4.7, perl/5.18.0/gcc-4.4.7

[Alchimic007]

Also, could you provide some DESCHRAMBLER requierements, or specifications, may be this way I could understand the core of the problem

[jkimlab]

It looks like our code is not compatible with your machine. I recommend using the CentOS or Ubuntu Linux machine.

On Oct 4, 2023, at 11:01 PM, Alchimic007 @.***> wrote:

About server specifications : Alces Software HPC Stack For Linux Based on Scientific Linux 6.5 Perl: perl/5.14.2/gcc-4.4.7, perl/5.18.0/gcc-4.4.7

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/16#issuecomment-1746939553, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV6OYNMFUMXUF6L6BJLX5VT47AVCNFSM6AAAAAA5REDPDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBWHEZTSNJVGM. You are receiving this because you commented.

[Alchimic007]

can I use virtual machine or environement instead because we have not got another machine

[Alchimic007]

Thank you for your help

[jkimlab]

I haven’t tried but it may work.

On Oct 4, 2023, at 11:16 PM, Alchimic007 @.***> wrote:

can I use virtual machine or environement instead because we have not got another machine

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/16#issuecomment-1746965670, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PVYBAASYBH2BDEMRXITX5VVSDAVCNFSM6AAAAAA5REDPDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBWHE3DKNRXGA. You are receiving this because you commented.

[Alchimic007]

One more question. Could you tell me min appropriate version of Ubuntu or CentOS

[jkimlab]

We are using Ubuntu 18.04. You can try it.

On Oct 4, 2023, at 11:34 PM, Alchimic007 @.***> wrote:

One more question. Could you tell me min appropriate version of Ubuntu or CentOS

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/16#issuecomment-1746979249, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV2TRRLPOZ7SDZPGHM3X5VXW5AVCNFSM6AAAAAA5REDPDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBWHE3TSMRUHE. You are receiving this because you commented.

[Alchimic007]

Thank you again

[Alchimic007]

Hello again. Thank you for earlier consultation. I have tried Ubuntu virtual machine 22.04 and 18.04. Perl on Ubuntu 18.04 was 5.26.1, and on 22.04 was 5.34. After launch I got these messages. Could you help me with this? Thank you

Constructing syntenic fragments

• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.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 chr2 .. in ref chr3 in ref chr1 ......
• adding outgroup spc3 in ref chr2 ..... in ref chr3 ... in ref chr1 .....
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net
• processing spc2.raw.segs
• getting segments from spc2.processed.segs
• adding descendent spc2 in ref chr2 .. in ref chr3 in ref chr1 ......
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net
• reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net
• processing spc3.raw.segs
• getting segments from spc3.processed.segs
• adding descendent spc3 in ref chr2 ..... in ref chr3 ... in ref chr1 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02);

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

• Totally 0 APCFs Segmentation fault (core dumped)

Also, I'm trying to launch DESCHRAMBLER on CentOS 6.8 now, I will reply if everything goes fine. Thank you again

[jkimlab]

Good news! That is the Perl version issue. Please check https://github.com/jkimlab/DESCHRAMBLER/issues/11.

On Oct 6, 2023, at 10:48 PM, Alchimic007 @.***> wrote:

Hello again. Thank you for earlier consultation. I have tried Ubuntu virtual machine 22.04 and 18.04. Perl on Ubuntu 18.04 was 5.26.1, and on 22.04 was 5.34. After launch I got these messages. Could you help me with this? Thank you

Constructing syntenic fragments

reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.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 chr2 .. in ref chr3 in ref chr1 ...... adding outgroup spc3 in ref chr2 ..... in ref chr3 ... in ref chr1 ..... reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr2.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr3.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc2/net/chr1.net processing spc2.raw.segs getting segments from spc2.processed.segs adding descendent spc2 in ref chr2 .. in ref chr3 in ref chr1 ...... reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr2.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr3.net reading /home/maksym/Downloads/DESCHRAMBLER/examples/chainNet/spc1/spc3/net/chr1.net processing spc3.raw.segs getting segments from spc3.processed.segs adding descendent spc3 in ref chr2 ..... in ref chr3 ... in ref chr1 ..... TREE ((spc1:0.02,spc2:0.02)@:0.02,spc3:0.02); UNIVERSAL does not export anything at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/maksym/Downloads/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 /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/estparJC.pl line 7. BEGIN failed--compilation aborted at /home/maksym/Downloads/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 /home/maksym/Downloads/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /home/maksym/Downloads/DESCHRAMBLER/APCFs.300K/SFs/block_consscores.txt UNIVERSAL does not export anything at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/maksym/Downloads/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 /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/split_weak_joins.pl line 7. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/split_weak_joins.pl line 7. UNIVERSAL does not export anything at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/TreeFunctionsI.pm line 94. BEGIN failed--compilation aborted at /home/maksym/Downloads/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 /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/Tree/Tree.pm line 111. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO/TreeEventBuilder.pm line 77. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/../lib/perl/Bio/TreeIO.pm line 90. Compilation failed in require at /home/maksym/Downloads/DESCHRAMBLER/script/join_splits.pl line 7. BEGIN failed--compilation aborted at /home/maksym/Downloads/DESCHRAMBLER/script/join_splits.pl line 7.

Totally 0 APCFs Segmentation fault (core dumped) Also, I'm trying to launch DESCHRAMBLER on CentOS 6.8 now, I will reply if everything goes fine. Thank you again

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/16#issuecomment-1750712454, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV67QYQSDPV4IAGDNTDX6ADZRAVCNFSM6AAAAAA5REDPDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQG4YTENBVGQ. You are receiving this because you commented.

[Alchimic007]

Wow, thanks. So all I need to do is replace BioPerl libraries you gave in #11 issue?

[jkimlab]

Yes.

On Oct 6, 2023, at 10:54 PM, Alchimic007 @.***> wrote:

Wow, thanks. So all I need to do is replace BioPerl libraries you gave in #11 https://github.com/jkimlab/DESCHRAMBLER/issues/11 issue?

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[Alchimic007]

Thank you, I'll try it now

[Alchimic007]

Yes, it works, thank you very much.

[jkimlab]

Good to hear that.

On Oct 6, 2023, at 11:06 PM, Alchimic007 @.***> wrote:

Yes, it works, thank you very much.

— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/16#issuecomment-1750739762, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PVYVC6GYWXUDBFEXXLLX6AF5JAVCNFSM6AAAAAA5REDPDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQG4ZTSNZWGI. You are receiving this because you commented.