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jkimlab / DESCHRAMBLER

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Segmentation fault #7

Closed xuyuannnn closed 2 years ago

xuyuannnn commented 2 years ago

I meet the same preblem: It tells me that: /bin/sh: line 1: 30026 Segmentation fault /data/home/xuyuan/biosoft/D/DESCHRAMBLER/code/makeBlocks/createGenomeFile config.file Conserved.Segments > Genomes.Order make: *** [Makefile:57: Genomes.Order] Error 139

the same preblem to following scripts: createGenomeFile makeConservedSegments orthoBlocksToOrders outgroupSegsToOrders

so , Is there a compilation error? What can I do about it? my gcc version is 4.8.5

thanks

jkimlab commented 2 years ago

What is your Linux version, and when did you see the error (compiling or running)?

xuyuannnn commented 2 years ago

What is your Linux version, and when did you see the error (compiling or running)?

Hi , my linux version is 3.10.0-1062.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) . when I run DESCHRAMBLER.pl that I see the error .

thanks

jkimlab commented 2 years ago

I assume that you are using CentOS 7. Can you show me all messages printed on a screen (i) when you recompile the program, and (ii) when you run it? You may need to run “make clean” before running “make” for the recompilation.

Thanks.

On Aug 23, 2021, at 11:58 AM, xuyuannnn @.***> wrote:

What is your Linux version, and when did you see the error (compiling or running)?

Hi , my linux version is 3.10.0-1062.el7.x86_64 @. @.>) . when I run DESCHRAMBLER.pl that I see the error .

thanks

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/7#issuecomment-903403515, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV7H4BSHFFSH72O556LT6G2NHANCNFSM5CR7VJ7Q. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email.

xuyuannnn commented 2 years ago

I assume that you are using CentOS 7. Can you show me all messages printed on a screen (i) when you recompile the program, and (ii) when you run it? You may need to run “make clean” before running “make” for the recompilation. Thanks. … On Aug 23, 2021, at 11:58 AM, xuyuannnn @.> wrote: What is your Linux version, and when did you see the error (compiling or running)? Hi , my linux version is 3.10.0-1062.el7.x86_64 @. @.***>) . when I run DESCHRAMBLER.pl that I see the error . thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV7H4BSHFFSH72O556LT6G2NHANCNFSM5CR7VJ7Q. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email.

Hi , I downloaded the code and compiled it , I will show all messages for you ,that is so much ,thanks for your help !

  1. when I redownloaded th0e code and compiled it

sed -e 's::/data/home/xuyuan/biosoft/DESCHRAMBLER/examples/chainNet:g' examples/config.SFs.tmp > examples/config.SFs cd lib/kent/src/lib && make make[1]: Entering directory '/data/home/xuyuan/biosoft/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 options.c: In function ‘validateOption’: options.c:53:11: warning: variable ‘discardMe’ set but not used [-Wunused-but-set-variable] long long discardMe = 0; ^ 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 '/data/home/xuyuan/biosoft/DESCHRAMBLER/lib/kent/src/lib' cd code/makeBlocks && make make[1]: Entering directory '/data/home/xuyuan/biosoft/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 '/data/home/xuyuan/biosoft/DESCHRAMBLER/code/makeBlocks' cd code && make make[1]: Entering directory '/data/home/xuyuan/biosoft/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 '/data/home/xuyuan/biosoft/DESCHRAMBLER/code'

2.when I run it:

0 Pa /data/home/xuyuan/biosoft/DESCHRAMBLER/my_data/tree.txt /data/home/xuyuan/biosoft/DESCHRAMBLER/APCFs.300K/SFs/bpdist.txt Estimate JC parameter: 0.0001 readline() on closed filehandle F at /data/home/xuyuan/biosoft/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /data/home/xuyuan/biosoft/DESCHRAMBLER/APCFs.300K/SFs/block_consscores.txt

jkimlab commented 2 years ago

I think there was no problem when compiling the code.

I suspect the chain/net files. Can you show me the list of files in the chain and net directory, separately, for one example species?

xuyuannnn commented 2 years ago

I think there was no problem when compiling the code.

I suspect the chain/net files. Can you show me the list of files in the chain and net directory, separately, for one example species?

sorry , I resend the message , Is that what you wanna see? thank you very much!

the chain directory of species 'Am' : -rw-rw-r-- 1 xuyuan xuyuan 2829232 Aug 21 23:42 Plotosus_anguillaris.01.chain -rw-rw-r-- 1 xuyuan xuyuan 2435836 Aug 21 23:42 Plotosus_anguillaris.02.chain -rw-rw-r-- 1 xuyuan xuyuan 2131858 Aug 21 23:42 Plotosus_anguillaris.03.chain -rw-rw-r-- 1 xuyuan xuyuan 2288540 Aug 21 23:42 Plotosus_anguillaris.04.chain -rw-rw-r-- 1 xuyuan xuyuan 2333150 Aug 21 23:42 Plotosus_anguillaris.05.chain -rw-rw-r-- 1 xuyuan xuyuan 2250637 Aug 21 23:42 Plotosus_anguillaris.06.chain -rw-rw-r-- 1 xuyuan xuyuan 2051162 Aug 21 23:42 Plotosus_anguillaris.07.chain -rw-rw-r-- 1 xuyuan xuyuan 1990882 Aug 21 23:42 Plotosus_anguillaris.08.chain -rw-rw-r-- 1 xuyuan xuyuan 2165889 Aug 21 23:42 Plotosus_anguillaris.09.chain -rw-rw-r-- 1 xuyuan xuyuan 2031128 Aug 21 23:42 Plotosus_anguillaris.10.chain -rw-rw-r-- 1 xuyuan xuyuan 2272987 Aug 21 23:42 Plotosus_anguillaris.11.chain -rw-rw-r-- 1 xuyuan xuyuan 2064855 Aug 21 23:42 Plotosus_anguillaris.12.chain -rw-rw-r-- 1 xuyuan xuyuan 2016185 Aug 21 23:42 Plotosus_anguillaris.13.chain -rw-rw-r-- 1 xuyuan xuyuan 1882999 Aug 21 23:42 Plotosus_anguillaris.14.chain -rw-rw-r-- 1 xuyuan xuyuan 1923860 Aug 21 23:42 Plotosus_anguillaris.15.chain -rw-rw-r-- 1 xuyuan xuyuan 2113038 Aug 21 23:42 Plotosus_anguillaris.16.chain -rw-rw-r-- 1 xuyuan xuyuan 1826856 Aug 21 23:42 Plotosus_anguillaris.17.chain -rw-rw-r-- 1 xuyuan xuyuan 1792802 Aug 21 23:42 Plotosus_anguillaris.18.chain -rw-rw-r-- 1 xuyuan xuyuan 1840548 Aug 21 23:42 Plotosus_anguillaris.19.chain -rw-rw-r-- 1 xuyuan xuyuan 1449855 Aug 21 23:42 Plotosus_anguillaris.20.chain -rw-rw-r-- 1 xuyuan xuyuan 1791142 Aug 21 23:42 Plotosus_anguillaris.21.chain -rw-rw-r-- 1 xuyuan xuyuan 1734185 Aug 21 23:42 Plotosus_anguillaris.22.chain -rw-rw-r-- 1 xuyuan xuyuan 1679508 Aug 21 23:42 Plotosus_anguillaris.23.chain -rw-rw-r-- 1 xuyuan xuyuan 1716957 Aug 21 23:42 Plotosus_anguillaris.24.chain

the net directory of 'Am': -rw-rw-r-- 1 xuyuan xuyuan 550824 Aug 21 23:42 chr10.net -rw-rw-r-- 1 xuyuan xuyuan 665316 Aug 21 23:42 chr11.net -rw-rw-r-- 1 xuyuan xuyuan 610303 Aug 21 23:42 chr12.net -rw-rw-r-- 1 xuyuan xuyuan 520065 Aug 21 23:42 chr13.net -rw-rw-r-- 1 xuyuan xuyuan 483312 Aug 21 23:42 chr14.net -rw-rw-r-- 1 xuyuan xuyuan 625573 Aug 21 23:42 chr15.net -rw-rw-r-- 1 xuyuan xuyuan 595045 Aug 21 23:42 chr16.net -rw-rw-r-- 1 xuyuan xuyuan 451708 Aug 21 23:42 chr17.net -rw-rw-r-- 1 xuyuan xuyuan 485979 Aug 21 23:42 chr18.net -rw-rw-r-- 1 xuyuan xuyuan 382454 Aug 21 23:42 chr19.net -rw-rw-r-- 1 xuyuan xuyuan 1018400 Aug 21 23:42 chr1.net -rw-rw-r-- 1 xuyuan xuyuan 425615 Aug 21 23:42 chr20.net -rw-rw-r-- 1 xuyuan xuyuan 321180 Aug 21 23:42 chr21.net -rw-rw-r-- 1 xuyuan xuyuan 410446 Aug 21 23:42 chr22.net -rw-rw-r-- 1 xuyuan xuyuan 417478 Aug 21 23:42 chr23.net -rw-rw-r-- 1 xuyuan xuyuan 428673 Aug 21 23:42 chr24.net -rw-rw-r-- 1 xuyuan xuyuan 915711 Aug 21 23:42 chr2.net -rw-rw-r-- 1 xuyuan xuyuan 635826 Aug 21 23:42 chr3.net -rw-rw-r-- 1 xuyuan xuyuan 693670 Aug 21 23:42 chr4.net -rw-rw-r-- 1 xuyuan xuyuan 874442 Aug 21 23:42 chr5.net -rw-rw-r-- 1 xuyuan xuyuan 688540 Aug 21 23:42 chr6.net -rw-rw-r-- 1 xuyuan xuyuan 533631 Aug 21 23:42 chr7.net -rw-rw-r-- 1 xuyuan xuyuan 614107 Aug 21 23:42 chr8.net -rw-rw-r-- 1 xuyuan xuyuan 728778 Aug 21 23:42 chr9.net

jkimlab commented 2 years ago

Yes, I found the reason.

The filenames in those two directories must be the same, and the filename needs to represent the name of the reference chromosome.

Please try to fix it, and run our program again.

Thanks.

xuyuannnn commented 2 years ago

Yes, I found the reason.

The filenames in those two directories must be the same, and the filename needs to represent the name of the reference chromosome.

Please try to fix it, and run our program again.

Thanks.

sorry , when I change my filanames to following , I see error again , program told that can not find file , It doesn't seem to recognize the number of filename . I have tried multiple forms of filenames , for instance ,'chr1.chain' and 'chr1.net' , 'Plotosus_anguillaris.01.chain' and 'Plotosus_anguillaris.01.net' , but error still occurs,

thanks !

now, my chain directory of species 'Am':

-rw-rw-r-- 1 xuyuan xuyuan 2829232 Aug 21 23:42 Plotosus_anguillaris.01.chain -rw-rw-r-- 1 xuyuan xuyuan 2435836 Aug 21 23:42 Plotosus_anguillaris.02.chain -rw-rw-r-- 1 xuyuan xuyuan 2131858 Aug 21 23:42 Plotosus_anguillaris.03.chain -rw-rw-r-- 1 xuyuan xuyuan 2288540 Aug 21 23:42 Plotosus_anguillaris.04.chain -rw-rw-r-- 1 xuyuan xuyuan 2333150 Aug 21 23:42 Plotosus_anguillaris.05.chain -rw-rw-r-- 1 xuyuan xuyuan 2250637 Aug 21 23:42 Plotosus_anguillaris.06.chain -rw-rw-r-- 1 xuyuan xuyuan 2051162 Aug 21 23:42 Plotosus_anguillaris.07.chain -rw-rw-r-- 1 xuyuan xuyuan 1990882 Aug 21 23:42 Plotosus_anguillaris.08.chain -rw-rw-r-- 1 xuyuan xuyuan 2165889 Aug 21 23:42 Plotosus_anguillaris.09.chain -rw-rw-r-- 1 xuyuan xuyuan 2031128 Aug 21 23:42 Plotosus_anguillaris.10.chain -rw-rw-r-- 1 xuyuan xuyuan 2272987 Aug 21 23:42 Plotosus_anguillaris.11.chain -rw-rw-r-- 1 xuyuan xuyuan 2064855 Aug 21 23:42 Plotosus_anguillaris.12.chain -rw-rw-r-- 1 xuyuan xuyuan 2016185 Aug 21 23:42 Plotosus_anguillaris.13.chain -rw-rw-r-- 1 xuyuan xuyuan 1882999 Aug 21 23:42 Plotosus_anguillaris.14.chain -rw-rw-r-- 1 xuyuan xuyuan 1923860 Aug 21 23:42 Plotosus_anguillaris.15.chain -rw-rw-r-- 1 xuyuan xuyuan 2113038 Aug 21 23:42 Plotosus_anguillaris.16.chain -rw-rw-r-- 1 xuyuan xuyuan 1826856 Aug 21 23:42 Plotosus_anguillaris.17.chain -rw-rw-r-- 1 xuyuan xuyuan 1792802 Aug 21 23:42 Plotosus_anguillaris.18.chain -rw-rw-r-- 1 xuyuan xuyuan 1840548 Aug 21 23:42 Plotosus_anguillaris.19.chain -rw-rw-r-- 1 xuyuan xuyuan 1449855 Aug 21 23:42 Plotosus_anguillaris.20.chain -rw-rw-r-- 1 xuyuan xuyuan 1791142 Aug 21 23:42 Plotosus_anguillaris.21.chain -rw-rw-r-- 1 xuyuan xuyuan 1734185 Aug 21 23:42 Plotosus_anguillaris.22.chain -rw-rw-r-- 1 xuyuan xuyuan 1679508 Aug 21 23:42 Plotosus_anguillaris.23.chain -rw-rw-r-- 1 xuyuan xuyuan 1716957 Aug 21 23:42 Plotosus_anguillaris.24.chain

net directory of 'Am': -rw-rw-r-- 1 xuyuan xuyuan 1018400 Aug 21 23:42 Plotosus_anguillaris.01.net -rw-rw-r-- 1 xuyuan xuyuan 915711 Aug 21 23:42 Plotosus_anguillaris.02.net -rw-rw-r-- 1 xuyuan xuyuan 635826 Aug 21 23:42 Plotosus_anguillaris.03.net -rw-rw-r-- 1 xuyuan xuyuan 693670 Aug 21 23:42 Plotosus_anguillaris.04.net -rw-rw-r-- 1 xuyuan xuyuan 874442 Aug 21 23:42 Plotosus_anguillaris.05.net -rw-rw-r-- 1 xuyuan xuyuan 688540 Aug 21 23:42 Plotosus_anguillaris.06.net -rw-rw-r-- 1 xuyuan xuyuan 533631 Aug 21 23:42 Plotosus_anguillaris.07.net -rw-rw-r-- 1 xuyuan xuyuan 614107 Aug 21 23:42 Plotosus_anguillaris.08.net -rw-rw-r-- 1 xuyuan xuyuan 728778 Aug 21 23:42 Plotosus_anguillaris.09.net -rw-rw-r-- 1 xuyuan xuyuan 550824 Aug 21 23:42 Plotosus_anguillaris.10.net -rw-rw-r-- 1 xuyuan xuyuan 665316 Aug 21 23:42 Plotosus_anguillaris.11.net -rw-rw-r-- 1 xuyuan xuyuan 610303 Aug 21 23:42 Plotosus_anguillaris.12.net -rw-rw-r-- 1 xuyuan xuyuan 520065 Aug 21 23:42 Plotosus_anguillaris.13.net -rw-rw-r-- 1 xuyuan xuyuan 483312 Aug 21 23:42 Plotosus_anguillaris.14.net -rw-rw-r-- 1 xuyuan xuyuan 625573 Aug 21 23:42 Plotosus_anguillaris.15.net -rw-rw-r-- 1 xuyuan xuyuan 595045 Aug 21 23:42 Plotosus_anguillaris.16.net -rw-rw-r-- 1 xuyuan xuyuan 451708 Aug 21 23:42 Plotosus_anguillaris.17.net -rw-rw-r-- 1 xuyuan xuyuan 485979 Aug 21 23:42 Plotosus_anguillaris.18.net -rw-rw-r-- 1 xuyuan xuyuan 382454 Aug 21 23:42 Plotosus_anguillaris.19.net -rw-rw-r-- 1 xuyuan xuyuan 425615 Aug 21 23:42 Plotosus_anguillaris.20.net -rw-rw-r-- 1 xuyuan xuyuan 321180 Aug 21 23:42 Plotosus_anguillaris.21.net -rw-rw-r-- 1 xuyuan xuyuan 410446 Aug 21 23:42 Plotosus_anguillaris.22.net -rw-rw-r-- 1 xuyuan xuyuan 417478 Aug 21 23:42 Plotosus_anguillaris.23.net -rw-rw-r-- 1 xuyuan xuyuan 428673 Aug 21 23:42 Plotosus_anguillaris.24.net

when I run it after I change the filenames

Constructing syntenic fragments

0 Pa /data/home/xuyuan/biosoft/DESCHRAMBLER/my_data/tree.txt /data/home/xuyuan/biosoft/DESCHRAMBLER/APCFs.300K/SFs/bpdist.txt Estimate JC parameter: 0.0001 readline() on closed filehandle F at /data/home/xuyuan/biosoft/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /data/home/xuyuan/biosoft/DESCHRAMBLER/APCFs.300K/SFs/block_consscores.txt

jkimlab commented 2 years ago

Simply changing filenames may not be a final solution. I recommend regenerating chain/net files, and try again. Thanks.

xuyuannnn commented 2 years ago

Simply changing filenames may not be a final solution. I recommend regenerating chain/net files, and try again. Thanks.

Ok , Thanks for your patient guidance! Thanks!